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kundajelab / chipseq_pipeline

AQUAS TF and histone ChIP-seq pipeline
BSD 3-Clause "New" or "Revised" License
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Fatal error: TF_chipseq_pipeline/modules/align_bwa.bds, line 87, pos 3. Task/s failed. #14

Closed rdali closed 7 years ago

rdali commented 7 years ago

Fatal error: TF_chipseq_pipeline/modules/align_bwa.bds, line 87, pos 3. Task/s failed. chipseq.bds, line 76 : main() chipseq.bds, line 79 : void main() { // chipseq pipeline starts here chipseq.bds, line 87 : align() // align and postalign chipseq.bds, line 318 : void align() { chipseq.bds, line 355 : for ( int ctl=0; ctl <= 1; ctl++) { // iterate through inputs (ctl==0 : exp. replicate, ctl==1 : control) chipseq.bds, line 358 : for ( int rep=1; rep <= get_num_rep( ctl ); rep++) { chipseq.bds, line 364 : if ( no_par ) align( ctl, rep, nth_rep{group} ) // parallel jobs for align() for each replicate and each control chipseq.bds, line 374 : void align( int ctl, int rep, int nth_rep ) { chipseq.bds, line 376 : if ( is_se( ctl, rep ) ) align_SE( ctl, rep, nth_rep ) chipseq.bds, line 377 : else align_PE( ctl, rep, nth_rep ) chipseq.bds, line 550 : void align_PE( int ctl, int rep, int nth_rep ) { chipseq.bds, line 563 : if ( is_inputfastq( ctl, rep ) ) { chipseq.bds, line 582 : if ( aligner == "bwa" ) { chipseq.bds, line 583 : ( bam, flagstatqc ) = bwa_PE( pooled_fastq_pair1, pooled_fastq_pair2, aln_o_dir, qc_o_dir, group, nth_rep ) align_bwa.bds, line 66 : string[] bwa_PE( string fastq1, string fastq2, string o_dir, string log_o_dir, string group, int nth_bwa ) { align_bwa.bds, line 76 : if ( out <- in ) { // compare file timestamps of in and out (to check if job is already done or not) align_bwa.bds, line 87 : wait

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. 00:00:51.033 Writing report file 'chipseq.bds.20170529_194354_069.report.html' 00:00:51.155 Program 'chipseq.bds.20170529_194354_069' finished, exit value: 1, tasks executed: 1, tasks failed: 1, tasks failed names: bwa_sam_PE rep1. 00:00:51.156 Finished. Exit code: 1 00:00:51.156 ExecutionerLocal 'Local[41]': Killed

leepc12 commented 7 years ago

Could you post a full STDOUT/STDERR and chipseq.bds.20170529_194354_069.report.html here?

rdali commented 7 years ago

STDOUT

== git info Latest git commit : f26ac9608ba2bdff10772b5cf24f0e3a259412b6 (Tue May 9 23:50:11 2017) Reading parameters from section (default) in file(tools/TF_chipseq_pipeline/default.env)...

== configuration file info Hostname : lm-1r16-n02.guillimin.clumeq.ca Configuration file : Environment file : tools/TF_chipseq_pipeline/default.env

Warning: Maximum # threads (-nth) for a pipeline is <= 1. Turning off parallelization... (-no_par)

== parallelization info No parallel jobs : true Maximum # threads : 1

== cluster/system info Walltime (general) : 5h50m Max. memory (general) : 7G Force to use a system : local Process priority (niceness) : 0 Retiral for failed tasks : 0 Submit tasks to a cluster queue : Unlimited cluster mem./walltime : false

== shell environment info Conda env. : aquas_chipseq Conda env. for python3 : aquas_chipseq_py3 Conda bin. directory :

Shell cmd. for init. : if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

Shell cmd. for init.(py3) : if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source activate aquas_chipseq_py3; sleep 5; fi; export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

Shell cmd. for fin. : TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

Cluster task min. len. : 60

Cluster task delay : 0

== output directory/title info Output dir. : project/ChIPSeq/160130_CTCF Title (prefix) : 160130_CTCF Reading parameters from section (default) in file(tools/TF_chipseq_pipeline/default.env)...

== species settings Species : hg19 Species file :

Species name (WashU browser) : hg19 Ref. genome seq. fasta : Chr. sizes file : tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes Black list bed : Ref. genome seq. dir. :

== ENCODE accession settings ENCODE experiment accession : ENCODE award RFA : ENCODE assay category : ENCODE assay title : ENCODE award : ENCODE lab : ENCODE assembly genome : ENCODE alias prefix : KLAB_PIPELINE

== report settings URL root for output directory : Genome coord. for browser tracks :

== align bwa settings Param. for bwa : -q 5 -l 32 -k 2 BWA index : tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa Walltime (bwa) : 47h Max. memory (bwa) : 12G

== align multimapping settings

alignments reported for multimapping : 0

== postalign bam settings MAPQ reads rm thresh. : 30 Rm. tag reads with str. : No dupe removal in filtering raw bam : false Walltime (bam filter) : 23h Max. memory (bam filter) : 12G Dup marker : picard Use sambamba markdup (instead of picard) : false

== postalign bed/tagalign settings Max. memory for UNIX shuf : 12G

== postalign cross-corr. analysis settings Max. memory for UNIX shuf : 12G User-defined cross-corr. peak strandshift : -1 Extra parameters for cross-corr. analysis :

== callpeak spp settings Threshold for # peak : 300000 Walltime (spp) : 47h Max. memory (spp) : 12G Stack size for run_spp.R : Use-defined cross-corr. peak strandshift; if -1, use frag. len. :-1 Extra parameters for run_spp.R :

== callpeak gem settings Threshold for # peak in GEM : 300000 Min. length of k-mers in GEM : 6 Max. length of k-mers in GEM : 13 Q-value threshold for GEM : 0.0 Read distribution txt for GEM : tools/TF_chipseq_pipeline/etc/Read_Distribution_default.txt Extra parameters for GEM : Walltime (GEM) : 47h Max. memory (GEM) : 15G

== callpeak PeakSeq settings Target FDR for PeakSeq :0.05 Number of simulations for PeakSeq :10 Enrichment mapped frag. len. for PeakSeq :-1 Minimum interpeak distance for PeakSeq :-1 Mappability map file for PeakSeq : Maximum Q-value for PeakSeq :0.1 Background model for PeakSeq :Simulated Extra parameters for PeakSeq : Walltime (PeakSeq) : 47h Max. memory (PeakSeq) : 12G

== callpeak macs2 settings Genome size (hs,mm) : hs Walltime (macs2) : 23h Max. memory (macs2) : 15G P-value cutoff (macs2 callpeak) : 0.01 --keep-dup (macs2 callpeak) : all --extsize (macs2 callpeak); if -1 then use frag. len. : -1 --shift (macs2 callpeak) : 0 Extra parameters for macs2 callpeak :

== callpeak naiver overlap settings Bedtools intersect -nonamecheck : false

== IDR settings Append IDR threshold to IDR out_dir : false

== chipseq pipeline settings

replicates : 1

Type of ChIP-Seq pipeline : TF Final stage for ChIP-Seq : peak Signal tracks for pooled rep. only : false Aligner to map raw reads : bwa

reads to subsample for cross-corr. analysis : 15000000

reads to subsample exp. replicates (0: no subsampling): 0

reads to subsample controls (0: no subsampling) : 0

Generate anonymized filt. bam : false Peak caller for IDR analysis : spp Control rep. depth ratio : 1.2 Scoring column for IDR : signal.value IDR threshold : 0.05 Force to use pooled ctl : false Peak calling for true reps only : false No peak calling for self pseudo reps : false Disable cross-correlation analysis : false Disable g. peak filt. thru. n. peak : false

== checking chipseq parameters ...

== checking input files ...

Rep1 fastq (PE) : project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq Control Rep1 fastq (PE) : project/ChIPSeq/HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq project/ChIPSeq/HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq Distributing 1 to ... {rep1=1, ctl1=1} Distributing 1 to ... [1, 1] bds -c tools/TF_chipseq_pipeline/bds.config -v tools/TF_chipseq_pipeline/chipseq.bds -title 160130_CTCF -final_stage peak -gensz hs -out_dir project/ChIPSeq/160130_CTCF -chrsz tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes -nth 1 -type TF -species hg19 -bwa_idx tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa -pe1 -fastq1_1:1 HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq -fastq1_2:1 HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq -ctl_pe1 -ctl_fastq1_1:1 HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq -ctl_fastq1_2:1 HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq

########################################################################

STDError

00:00:00.000 Bds 0.99999e (build 2016-08-26 06:34), by Pablo Cingolani 00:00:00.294 Parsing 00:00:15.989 Initializing 00:00:16.077 Process ID: chipseq.bds.20170529_194354_069 00:00:16.082 Running 00:00:23.200 Executioner factory: Creating new executioner type 'LOCAL' 00:00:23.336 ExecutionerLocal 'Local[41]': Queuing task: chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10 00:00:23.337 Waiting for all tasks to finish. 00:00:23.338 Wait: Waiting for task to finish: chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10, state: SCHEDULED 00:00:23.340 ExecutionerLocal 'Local[41]': Started running 00:00:23.342 ExecutionerLocal 'Local[41]': Task selected 'chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' on host 'localhost' [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [bwt_restore_sa] fail to open file 'tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa.sa' : No such file or directory Task failed: Program & line : 'tools/TF_chipseq_pipeline/modules/align_bwa.bds', line 181 Task Name : 'bwa_sam_PE rep1' Task ID : 'chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' Task PID : '31877' Task hint : 'bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai project/ChIPSeq/160130_CTCF/align/re' Task resources : 'cpus: 1 mem: -1.0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq, project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq, project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai, project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.sai]' Output files : '[project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam, project/ChIPSeq/160130_CTCF/qc/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.flagstat.qc]' Script file : 'project/ChIPSeq/chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10.sh' Exit status : '1' Program : 

    # SYS command. line 183

     if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

    # SYS command. line 185

     bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.sai project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq | pigz -p 1 -nc > project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz

    # SYS command. line 194

     pigz -p 1 -cd project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz \
                | awk 'BEGIN {FS="\t" ; OFS="\t"} ! /^@/ && $6!="*" { cigar=$6; gsub("[0-9]+D","",cigar); n = split(cigar,vals,"[A-Z]"); s = 0; for (i=1;i<=n;i++) s=s+vals[i]; seqlen=length($10) ; if (s!=seqlen) print $1"\t"; }' \
                | sort | uniq > project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads

    # SYS command. line 199

     if [ $(cat project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads | wc -l) -gt 0 ]; then \
                    zcat project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz | grep -v -F -f project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads | samtools view -Su - | samtools sort - project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE; \
                else \
                    samtools view -Su project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz | samtools sort - project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE; \
                fi

    # SYS command. line 211

     samtools flagstat project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam > project/ChIPSeq/160130_CTCF/qc/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.flagstat.qc

    # SYS command. line 212

     samtools index project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam

    # SYS command. line 216

     rm -f project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz

    # SYS command. line 218

     TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
StdErr (100000000 lines)  :
    [bwa_read_seq] 0.0% bases are trimmed.
    [bwa_read_seq] 0.1% bases are trimmed.
    [bwa_sai2sam_pe_core] convert to sequence coordinate... 
    [bwt_restore_sa] fail to open file 'tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa.sa' : No such file or directory

00:00:50.885 Wait: Task 'chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' finished. Fatal error: tools/TF_chipseq_pipeline/modules/align_bwa.bds, line 87, pos 3. Task/s failed. chipseq.bds, line 76 : main() chipseq.bds, line 79 : void main() { // chipseq pipeline starts here chipseq.bds, line 87 : align() // align and postalign chipseq.bds, line 318 : void align() { chipseq.bds, line 355 : for ( int ctl=0; ctl <= 1; ctl++) { // iterate through inputs (ctl==0 : exp. replicate, ctl==1 : control) chipseq.bds, line 358 : for ( int rep=1; rep <= get_num_rep( ctl ); rep++) { chipseq.bds, line 364 : if ( no_par ) align( ctl, rep, nth_rep{group} ) // parallel jobs for align() for each replicate and each control chipseq.bds, line 374 : void align( int ctl, int rep, int nth_rep ) { chipseq.bds, line 376 : if ( is_se( ctl, rep ) ) align_SE( ctl, rep, nth_rep ) chipseq.bds, line 377 : else align_PE( ctl, rep, nth_rep ) chipseq.bds, line 550 : void align_PE( int ctl, int rep, int nth_rep ) { chipseq.bds, line 563 : if ( is_inputfastq( ctl, rep ) ) { chipseq.bds, line 582 : if ( aligner == "bwa" ) { chipseq.bds, line 583 : ( bam, flagstatqc ) = bwa_PE( pooled_fastq_pair1, pooled_fastq_pair2, aln_o_dir, qc_o_dir, group, nth_rep ) align_bwa.bds, line 66 : string[] bwa_PE( string fastq1, string fastq2, string o_dir, string log_o_dir, string group, int nth_bwa ) { align_bwa.bds, line 76 : if ( out <- in ) { // compare file timestamps of in and out (to check if job is already done or not) align_bwa.bds, line 87 : wait

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. 00:00:51.033 Writing report file 'chipseq.bds.20170529_194354_069.report.html' 00:00:51.155 Program 'chipseq.bds.20170529_194354_069' finished, exit value: 1, tasks executed: 1, tasks failed: 1, tasks failed names: bwa_sam_PE rep1. 00:00:51.156 Finished. Exit code: 1 00:00:51.156 ExecutionerLocal 'Local[41]': Killed

############################################################################

cat chipseq.bds.20170529_194354_069.report.html

BigDataScript report: chipseq.bds

Script file tools/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170529_194354_069
Start time 2017-05-29 19:43:54
Run time 00:00:34.931
Tasks executed 1
Tasks failed 1
Tasks failed names 
bwa_sam_PE rep1
Arguments* [-title, 160130_CTCF, -final_stage, peak, -gensz, hs, -out_dir, project/ChIPSeq/160130_CTCF, -chrsz, tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes, -nth, 1, -type, TF, -species, hg19, -bwa_idx, tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa, -pe1, -fastq1_1:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq, -fastq1_2:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq, -ctl_pe1, -ctl_fastq1_1:1, HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq, -ctl_fastq1_2:1, HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq]
System* local
Cpus* -1
Exit value 1
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None 
 chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.align_bwa.bwa_sam_PE_rep1.line_181.id_10
Name bwa_sam_PE rep1
Thread thread_Root
PID 31877
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus 1
Mem
Start 2017-05-29 19:44:01
End 2017-05-29 19:44:01
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.sai
Output files project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam project/ChIPSeq/160130_CTCF/qc/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.flagstat.qc
Dependencies 
 
# SYS command. line 183

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 185

 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.sai project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq | pigz -p 1 -nc > project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz

# SYS command. line 194

 pigz -p 1 -cd project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz \
            | awk 'BEGIN {FS="\t" ; OFS="\t"} ! /^@/ && $6!="*" { cigar=$6; gsub("[0-9]+D","",cigar); n = split(cigar,vals,"[A-Z]"); s = 0; for (i=1;i<=n;i++) s=s+vals[i]; seqlen=length($10) ; if (s!=seqlen) print $1"\t"; }' \
            | sort | uniq > project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads

# SYS command. line 199

 if [ $(cat project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads | wc -l) -gt 0 ]; then \
                zcat project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz | grep -v -F -f project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads | samtools view -Su - | samtools sort - project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE; \
            else \
                samtools view -Su project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz | samtools sort - project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE; \
            fi

# SYS command. line 211

 samtools flagstat project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam > project/ChIPSeq/160130_CTCF/qc/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.flagstat.qc

# SYS command. line 212

 samtools index project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam

# SYS command. line 216

 rm -f project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz

# SYS command. line 218

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
 
    
--------------------Stderr--------------------
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[bwt_restore_sa] fail to open file 'tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa.sa' : No such file or directory

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /home/rdali/.bds/bds
string _LMFILES_ /sb/software/CentOS-6/tools/Modules/3.2.9/modulefiles/perl/5.16:/sb/software/CentOS-6/eb/modules/all/Core/Java/1.8.0_45.lua
string _ModuleTable001_ 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
string _ModuleTable002_ 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
string _ModuleTable003_ bGwvTGludXgiLCIvc2Ivc29mdHdhcmUvQ2VudE9TLTYvZWIvbW9kdWxlcy9hbGwvQ29yZSIsIi9zYi9ob21lL3JkYWxpL21vZHVsZWZpbGVzIix9LFsic3lzdGVtQmFzZU1QQVRIIl09Ii9zYi9zb2Z0d2FyZS9DZW50T1MtNi90b29scy9Nb2R1bGVzLzMuMi45L21vZHVsZWZpbGVzOi9zYi9zb2Z0d2FyZS9DZW50T1MtNi9lYi9tb2R1bGVzL2FsbC9MaW51eDovc2Ivc29mdHdhcmUvQ2VudE9TLTYvZWIvbW9kdWxlcy9hbGwvQ29yZTovc2IvaG9tZS9yZGFsaS9tb2R1bGVmaWxlcyIsWyJ2ZXJzaW9uIl09Mix9
string _ModuleTable_Sz_ 3
bool allowEmpty false
string[] args [-title, 160130_CTCF, -final_stage, peak, -gensz, hs, -out_dir, project/ChIPSeq/160130_CTCF, -chrsz, tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes, -nth, 1, -type, TF, -species, hg19, -bwa_idx, tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa, -pe1, -fastq1_1:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq, -fastq1_2:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq, -ctl_pe1, -ctl_fastq1_1:1, HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq, -ctl_fastq1_2:1, HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq]
string BASH_ENV /software/CentOS-6/tools/lmod/lmod/init/bash
string BASH_FUNC_ml() () { eval $($LMOD_DIR/ml_cmd \"$@\")\n}
string BASH_FUNC_module() () { eval $($LMOD_CMD bash \"$@\");\n [ $? = 0 ] && eval $(${LMOD_SETTARG_CMD:-:} -s sh)\n}
bool canFail false
string CONDA_DEFAULT_ENV aquas_chipseq
string CONDA_PATH_BACKUP tools/miniconda3/bin:tools/perl5/bin:/software/CentOS-6/tools/perl-5.16/bin:/opt/torque/x86_64/bin:/usr/lib64/qt-3.3/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:tools:tools/cmake-3.4.1/bin:tools/circos-0.68/bin:tools/MACS-1.4.2/bin:tools/bam-readcount/build/bin:tools/HTSeq-0.6.1/scripts:tools/bowtie-1.1.1:tools/hicup_v0.5.3:/usr/bin/gnuplot:tools/hdf5-1.8.14/bin:/home/rdali/tools/pythonPackages/bin:/home/rdali/tools/pythonPackages:/home/rdali/tools/tabix-0.2.6:/home/rdali/tools/vcftools_0.1.12b/perl:/home/rdali/tools/samtools-0.1.19/bcftools:/home/rdali/tools/IGVTools:/home/rdali/tools/novocraft:/home/rdali/tools/bowtie2-2.1.0:/home/rdali/tools/tophat-2.0.11.Linux_x86_64:/home/rdali/tools/samtools-0.1.19:/home/rdali/.aspera/connect/bin:/home/rdali/tools/FastQC:/home/rdali/tools/cutadapt-1.4.1/bin:/home/rdali/tools:/home/rdali/software/bin:/home/rdali/tools/sratoolkit.2.3.5-2-centos_linux64/bin:/home/rdali/tools/bedtools-2.17.0/bin:/home/rdali/tools/bwa-0.7.10:/home/rdali/tools/mySoftwareLibs:/home/rdali/tools/ghostscript-9.15/bin:/home/rdali/tools/weblogo:tools/homer/bin:/sb/home/rdali/.local/lib/python2.7/site-packages:/home/rdali/.bds:/home/rdali/bin
string CONDA_PREFIX tools/miniconda3/envs/aquas_chipseq
string CONDA_PS1_BACKUP
string CPATH /software/CentOS-6/eb/software/Core/Java/1.8.0_45/include
int cpus -1
int cpusLocal 32
string CVS_RSH ssh
int day 86400
real E 2.718281828459045
string EBDEVELJAVA /software/CentOS-6/eb/software/Core/Java/1.8.0_45/easybuild/Core-Java-1.8.0_45-easybuild-devel
string EBROOTJAVA /software/CentOS-6/eb/software/Core/Java/1.8.0_45
string EBVERSIONJAVA 1.8.0_45
string ENVIRONMENT BATCH
int G 1073741824
string G_BROKEN_FILENAMES 1
string HDF5_DIR tools/hdf5-1.8.14/bin
string HISTCONTROL ignoreboth:erasedups
string HISTIGNORE ls:pwd:logout:rm*:mkdir*:rdali:hic:q
string HISTSIZE 1000000
string HISTTIMEFORMAT %F %T
string HOME /home/rdali
string HOSTNAME lm-1r16-n02
int hour 3600
string JAVA_HOME /software/CentOS-6/eb/software/Core/Java/1.8.0_45
int K 1024
string LANG C
string LD_LIBRARY_PATH /gs/software/CentOS-6/eb/software/Core/Java/1.8.0_45/jre/lib/amd64/server:/gs/software/CentOS-6/eb/software/Core/Java/1.8.0_45/jre/lib/amd64:/gs/software/CentOS-6/eb/software/Core/Java/1.8.0_45/jre/../lib/amd64:/software/CentOS-6/eb/software/Core/Java/1.8.0_45/lib:$LD_LIBRARY_PATH:~/software/lib:/home/rdali/software/lib:tools/hdf5-1.8.14/lib/:/home/rdali/tools/ghmm-0.9-rc3/lib:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/runtime/glnxa64:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/bin/glnxa64:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/server:~/software/lib:/home/rdali/software/lib:tools/hdf5-1.8.14/lib:/home/rdali/tools/ghmm-0.9-rc3/lib:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/runtime/glnxa64:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/bin/glnxa64:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/server
string LESSOPEN ||/usr/bin/lesspipe.sh %s
string LIBRARY_PATH /software/CentOS-6/eb/software/Core/Java/1.8.0_45/lib
string LMOD_arch x86_64
string LMOD_CMD /software/CentOS-6/tools/lmod/lmod/libexec/lmod
string LMOD_COLORIZE yes
string LMOD_DEFAULT_MODULEPATH /sb/software/CentOS-6/tools/Modules/3.2.9/modulefiles:/sb/software/CentOS-6/eb/modules/all/Linux:/sb/software/CentOS-6/eb/modules/all/Core:/sb/home/rdali/modulefiles
string LMOD_DIR /software/CentOS-6/tools/lmod/lmod/libexec
string LMOD_FULL_SETTARG_SUPPORT no
string LMOD_PKG /software/CentOS-6/tools/lmod/lmod
string LMOD_PREPEND_BLOCK normal
string LMOD_SETTARG_CMD :
string LMOD_sys Linux
string LMOD_VERSION 6.1
string LOADEDMODULES perl/5.16:Java/1.8.0_45
string LOGNAME rdali
string LSCRATCH /localscratch/91162790.gm-1r16-n04.guillimin.clumeq.ca
int M 1048576
string MAIL /var/spool/mail/rdali
string MANPATH /software/CentOS-6/eb/software/Core/Java/1.8.0_45/man:/software/CentOS-6/tools/perl-5.16/man:/software/CentOS-6/tools/lmod/lmod/share/man::
int mem -1
int minute 60
string MODULEPATH /sb/software/CentOS-6/tools/Modules/3.2.9/modulefiles:/sb/software/CentOS-6/eb/modules/all/Linux:/sb/software/CentOS-6/eb/modules/all/Core:/sb/home/rdali/modulefiles
string MODULEPATH_ROOT /sb/software/CentOS-6/eb/modules/all
string MODULESHOME /software/CentOS-6/tools/lmod/lmod
string NLSPATH /usr/dt/lib/nls/msg/%L/%N.cat
string node
int P 1125899906842624
string PATH /software/CentOS-6/eb/software/Core/Java/1.8.0_45:/software/CentOS-6/eb/software/Core/Java/1.8.0_45/bin:tools/miniconda3/envs/aquas_chipseq/extra/phantompeakqualtools:tools/miniconda3/envs/aquas_chipseq/bin:tools/miniconda3/bin:tools/perl5/bin:/software/CentOS-6/tools/perl-5.16/bin:/opt/torque/x86_64/bin:/usr/lib64/qt-3.3/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:tools:tools/cmake-3.4.1/bin:tools/circos-0.68/bin:tools/MACS-1.4.2/bin:tools/bam-readcount/build/bin:tools/HTSeq-0.6.1/scripts:tools/bowtie-1.1.1:tools/hicup_v0.5.3:/usr/bin/gnuplot:tools/hdf5-1.8.14/bin:/home/rdali/tools/pythonPackages/bin:/home/rdali/tools/pythonPackages:/home/rdali/tools/tabix-0.2.6:/home/rdali/tools/vcftools_0.1.12b/perl:/home/rdali/tools/samtools-0.1.19/bcftools:/home/rdali/tools/IGVTools:/home/rdali/tools/novocraft:/home/rdali/tools/bowtie2-2.1.0:/home/rdali/tools/tophat-2.0.11.Linux_x86_64:/home/rdali/tools/samtools-0.1.19:/home/rdali/.aspera/connect/bin:/home/rdali/tools/FastQC:/home/rdali/tools/cutadapt-1.4.1/bin:/home/rdali/tools:/home/rdali/software/bin:/home/rdali/tools/sratoolkit.2.3.5-2-centos_linux64/bin:/home/rdali/tools/bedtools-2.17.0/bin:/home/rdali/tools/bwa-0.7.10:/home/rdali/tools/mySoftwareLibs:/home/rdali/tools/ghostscript-9.15/bin:/home/rdali/tools/weblogo:tools/homer/bin:/sb/home/rdali/.local/lib/python2.7/site-packages:/home/rdali/.bds:/home/rdali/bin:tools/miniconda3/envs/aquas_chipseq/extra/align2rawsignal/bin
string PBS_ENVIRONMENT PBS_BATCH
string PBS_GPUFILE /var/spool/pbs/aux//91162790.gm-1r16-n04.guillimin.clumeq.cagpu
string PBS_JOBCOOKIE 9AA928B60B64CD98E7E1F385AD8E7205
string PBS_JOBID 91162790.gm-1r16-n04.guillimin.clumeq.ca
string PBS_JOBNAME AQUAS-160130_CTCF
string PBS_MICFILE /var/spool/pbs/aux//91162790.gm-1r16-n04.guillimin.clumeq.camic
string PBS_MOMPORT 15003
string PBS_NODEFILE /var/spool/pbs/aux//91162790.gm-1r16-n04.guillimin.clumeq.ca
string PBS_NODENUM 0
string PBS_NP 1
string PBS_NUM_NODES 1
string PBS_NUM_PPN 1
string PBS_O_HOME /home/rdali
string PBS_O_HOST lg-1r17-n04.guillimin.clumeq.ca
string PBS_O_LANG en_CA.UTF-8
string PBS_O_LOGNAME rdali
string PBS_O_MAIL /var/spool/mail/rdali
string PBS_O_PATH tools/miniconda3/bin:tools/perl5/bin:/software/CentOS-6/tools/perl-5.16/bin:/opt/torque/x86_64/bin:/usr/lib64/qt-3.3/bin:/opt/moab/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:/sb/software/tools/scripts:/usr/lpp/mmfs/bin:/usr/lpp/mmfs/bin:tools:tools/cmake-3.4.1/bin:tools/circos-0.68/bin:tools/MACS-1.4.2/bin:tools/bam-readcount/build/bin:tools/HTSeq-0.6.1/scripts:tools/bowtie-1.1.1:tools/hicup_v0.5.3:/usr/bin/gnuplot:tools/hdf5-1.8.14/bin:/home/rdali/tools/pythonPackages/bin:/home/rdali/tools/pythonPackages:/home/rdali/tools/tabix-0.2.6:/home/rdali/tools/vcftools_0.1.12b/perl:/home/rdali/tools/samtools-0.1.19/bcftools:/home/rdali/tools/IGVTools:/home/rdali/tools/novocraft:/home/rdali/tools/bowtie2-2.1.0:/home/rdali/tools/tophat-2.0.11.Linux_x86_64:/home/rdali/tools/samtools-0.1.19:/home/rdali/.aspera/connect/bin:/home/rdali/tools/FastQC:/home/rdali/tools/cutadapt-1.4.1/bin:/home/rdali/tools:/home/rdali/software/bin:/home/rdali/tools/sratoolkit.2.3.5-2-centos_linux64/bin:/home/rdali/tools/bedtools-2.17.0/bin:/home/rdali/tools/bwa-0.7.10:/home/rdali/tools/mySoftwareLibs:/home/rdali/tools/ghostscript-9.15/bin:/home/rdali/tools/weblogo:tools/homer/bin:/sb/home/rdali/.local/lib/python2.7/site-packages:/home/rdali/.bds:/home/rdali/bin
string PBS_O_QUEUE metaq
string PBS_O_SERVER gm-schrmat
string PBS_O_SHELL /bin/bash
string PBS_O_SUBMIT_FILTER /opt/torque/x86_64/libexec/qsub_filter
string PBS_O_WORKDIR project/ChIPSeq
string PBS_QUEUE xlm2
string PBS_TASKNUM 1
string PBS_VERSION TORQUE-5.1.3
string PBS_VNODENUM 0
string PBS_WALLTIME 86400
string PBSCOREDUMP 1
string PERL5LIB tools/perl5/lib/perl5:/home/rdali/tools/vcftools_0.1.12b/perl
string PERL_LOCAL_LIB_ROOT tools/perl5
string PERL_MB_OPT --install_base \"tools/perl5\"
string PERL_MM_OPT INSTALL_BASE=tools/perl5
real PI 3.141592653589793
string ppwd project/ChIPSeq
string programName chipseq.bds
string programPath tools/TF_chipseq_pipeline/chipseq.bds
string PROMPT_COMMAND history -a
string PWD project/ChIPSeq
string QTDIR /usr/lib64/qt-3.3
string QTINC /usr/lib64/qt-3.3/include
string QTLIB /usr/lib64/qt-3.3/lib
string queue
string R_LIBS tools/R_LIBS
string RAMDISK /dev/shm/91162790.gm-1r16-n04.guillimin.clumeq.ca
int retry 0
string SCRATCH /gs/scratch/rdali
string SHELL /bin/bash
string SHLVL 3
string SSH_ASKPASS /usr/libexec/openssh/gnome-ssh-askpass
string system local
int T 1099511627776
int timeout -1
string USER rdali
string VDB_PWFILE keys/prj_6419.ngc
int walltimeout 8640000
int week 604800
string XAPPLRESDIR tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/X11/app-defaults
string XFILESEARCHPATH /usr/dt/app-defaults/%L/Dt
leepc12 commented 7 years ago

Did you use install_genome_data.sh for genome data installation? What files do you have in tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index?

rdali commented 7 years ago

I did use the install_genome_data.sh. I followed the instructions on github.

I have the following files: total 3.7G lrwxrwxrwx male.hg19.fa -> ../male.hg19.fa -rw-r--r-- male.hg19.fa.bwt -rw-r--r-- male.hg19.fa.pac -rw-r--r-- male.hg19.fa.ann -rw-r--r-- male.hg19.fa.amb

leepc12 commented 7 years ago

It looks like BWA index is not installed correctly. You need one more file on it (male.hg19.fa.sa). Did you see any error while running install_genome_data.sh?

rdali commented 7 years ago

None that I can recall. I am running it again and I will re-run the pipeline and will report back when it is done.

rdali commented 7 years ago

So I reran the install_genome_data.sh and now the male.hg19.fa.sa is installed, however, I still get an error; see below:

################################### STDERR for Genome Installation ################################### ################################### STDERR for Genome Installation ################################### ################################### STDERR for Genome Installation ###################################

--2017-06-02 08:53:47-- http://mitra.stanford.edu/kundaje/genome_data/hg19/globalmap_k20tok54.tgz Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable

The file is already fully retrieved; nothing to do.

--2017-06-02 08:53:47-- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/referenceSequences/male.hg19.fa.gz Resolving hgdownload.cse.ucsc.edu... 128.114.119.163 Connecting to hgdownload.cse.ucsc.edu|128.114.119.163|:80... connected. HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable

The file is already fully retrieved; nothing to do.

--2017-06-02 08:53:48-- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz Resolving hgdownload.cse.ucsc.edu... 128.114.119.163 Connecting to hgdownload.cse.ucsc.edu|128.114.119.163|:80... connected. HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable

The file is already fully retrieved; nothing to do.

--2017-06-02 08:53:48-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/hg19_gencode_tss_unique.bed.gz Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable

The file is already fully retrieved; nothing to do.

--2017-06-02 08:53:48-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable

The file is already fully retrieved; nothing to do.

--2017-06-02 08:53:48-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/reg2map_honeybadger2_dnase_prom_p2.bed.gz Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable

The file is already fully retrieved; nothing to do.

--2017-06-02 08:53:48-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/reg2map_honeybadger2_dnase_enh_p2.bed.gz Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable

The file is already fully retrieved; nothing to do.

--2017-06-02 08:53:48-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/dnase_avgs_reg2map_p10_merged_named.pvals.gz Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable

The file is already fully retrieved; nothing to do.

--2017-06-02 08:53:48-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/eid_to_mnemonic.txt Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable

The file is already fully retrieved; nothing to do.

tar: globalmap_k20tok54: skipping existing file tar: globalmap_k20tok54/chr17.uint8.unique: skipping existing file tar: globalmap_k20tok54/chrY.uint8.unique: skipping existing file tar: globalmap_k20tok54/chrM.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr22.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr12.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr2.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr18.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr15.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr9.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr19.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr6.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr13.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr10.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr20.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr21.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr8.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr7.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr4.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr1.uint8.unique: skipping existing file tar: globalmap_k20tok54/chrX.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr14.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr3.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr11.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr16.uint8.unique: skipping existing file tar: globalmap_k20tok54/chr5.uint8.unique: skipping existing file [bwa_index] Pack FASTA... 37.49 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=6191387966, availableWord=447648912 [BWTIncConstructFromPacked] 10 iterations done. 99999998 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999998 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 299999998 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 399999998 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 499999998 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 599999998 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 699999998 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 799999998 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 899999998 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 999999998 characters processed. [BWTIncConstructFromPacked] 110 iterations done. 1099999998 characters processed. 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[BWTIncConstructFromPacked] 600 iterations done. 5884897502 characters processed. [BWTIncConstructFromPacked] 610 iterations done. 5938212670 characters processed. [BWTIncConstructFromPacked] 620 iterations done. 5985595326 characters processed. [BWTIncConstructFromPacked] 630 iterations done. 6027705102 characters processed. [BWTIncConstructFromPacked] 640 iterations done. 6065128334 characters processed. [BWTIncConstructFromPacked] 650 iterations done. 6098386190 characters processed. [BWTIncConstructFromPacked] 660 iterations done. 6127941854 characters processed. [BWTIncConstructFromPacked] 670 iterations done. 6154206942 characters processed. [BWTIncConstructFromPacked] 680 iterations done. 6177547390 characters processed. [bwa_index] 3584.13 seconds elapse. [bwa_index] Update BWT... 21.54 sec [bwa_index] Pack forward-only FASTA... 24.44 sec [bwa_index] Construct SA from BWT and Occ... 968.91 sec [main] Version: 0.7.13-r1126 [main] CMD: bwa index male.hg19.fa [main] Real time: 4697.887 sec; CPU: 4636.520 sec

################################### STDOUT for Genome Installation ################################### ################################### STDOUT for Genome Installation ################################### ################################### STDOUT for Genome Installation ###################################

tools/TF_chipseq_pipeline/Genomes

Downloading files... globalmap_k20tok54/ globalmap_k20tok54/chr17.uint8.unique globalmap_k20tok54/chrY.uint8.unique globalmap_k20tok54/chrM.uint8.unique globalmap_k20tok54/chr22.uint8.unique globalmap_k20tok54/chr12.uint8.unique globalmap_k20tok54/chr2.uint8.unique globalmap_k20tok54/chr18.uint8.unique globalmap_k20tok54/chr15.uint8.unique globalmap_k20tok54/chr9.uint8.unique globalmap_k20tok54/chr19.uint8.unique globalmap_k20tok54/chr6.uint8.unique globalmap_k20tok54/chr13.uint8.unique globalmap_k20tok54/chr10.uint8.unique globalmap_k20tok54/chr20.uint8.unique globalmap_k20tok54/chr21.uint8.unique globalmap_k20tok54/chr8.uint8.unique globalmap_k20tok54/chr7.uint8.unique globalmap_k20tok54/chr4.uint8.unique globalmap_k20tok54/chr1.uint8.unique globalmap_k20tok54/chrX.uint8.unique globalmap_k20tok54/chr14.uint8.unique globalmap_k20tok54/chr3.uint8.unique globalmap_k20tok54/chr11.uint8.unique globalmap_k20tok54/chr16.uint8.unique globalmap_k20tok54/chr5.uint8.unique Extracting/processing data files... Building bwa index... [bwt_gen] Finished constructing BWT in 687 iterations. Creating species file... (tools/TF_chipseq_pipeline/Genomes/aquas_chipseq_species.conf) === Genome data (hg19) has been successfully installed. ===

################################### content of the Genomes/hg19/bwa_index ################################### ################################### content of the Genomes/hg19/bwa_index ################################### ################################### content of the Genomes/hg19/bwa_index ###################################

$ ls -ltrh Genomes/hg19/bwa_index/ total 5.1G lrwxrwxrwx 1 15 Jun 2 09:01 male.hg19.fa -> ../male.hg19.fa -rw-r--r-- 1 2.9G Jun 2 10:02 male.hg19.fa.bwt -rw-r--r-- 1 739M Jun 2 10:03 male.hg19.fa.pac -rw-r--r-- 1 944 Jun 2 10:03 male.hg19.fa.ann -rw-r--r-- 1 6.4K Jun 2 10:03 male.hg19.fa.amb -rw-r--r-- 1 1.5G Jun 2 10:19 male.hg19.fa.sa

rdali commented 7 years ago

################################### STDERROR of ChIPSeq pipeline ################################### ################################### STDERROR of ChIPSeq pipeline ################################### ################################### STDERROR of ChIPSeq pipeline ###################################

00:00:00.000 Bds 0.99999e (build 2016-08-26 06:34), by Pablo Cingolani 00:00:00.214 Parsing 00:00:13.628 Initializing 00:00:13.704 Process ID: chipseq.bds.20170602_104615_132 00:00:13.704 Running 00:00:21.261 Executioner factory: Creating new executioner type 'LOCAL' 00:00:21.340 ExecutionerLocal 'Local[38]': Queuing task: chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10 00:00:21.341 Waiting for all tasks to finish. 00:00:21.341 Wait: Waiting for task to finish: chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10, state: SCHEDULED 00:00:21.343 ExecutionerLocal 'Local[38]': Started running 00:00:21.344 ExecutionerLocal 'Local[38]': Task selected 'chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' on host 'localhost' [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 225438 pairs: 243.286 +/- 54.364 [infer_isize] skewness: 0.538; kurtosis: 0.215; ap_prior: 5.31e-05 [infer_isize] inferred maximum insert size: 621 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 5.77 sec [bwa_sai2sam_pe_core] changing coordinates of 3673 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9767 out of 10967 Q17 singletons are mated. [bwa_paired_sw] 294 out of 2210 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.18 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.01 sec [bwa_sai2sam_pe_core] print alignments... 1.41 sec [bwa_sai2sam_pe_core] 262144 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 241492 pairs: 242.723 +/- 54.198 [infer_isize] skewness: 0.537; kurtosis: 0.219; ap_prior: 5.16e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.51 sec [bwa_sai2sam_pe_core] changing coordinates of 1098 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9024 out of 10229 Q17 singletons are mated. [bwa_paired_sw] 41 out of 2130 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.07 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.82 sec [bwa_sai2sam_pe_core] print alignments... 00:01:22.625 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:01:22.879 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
1.40 sec [bwa_sai2sam_pe_core] 524288 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 240809 pairs: 241.415 +/- 54.160 [infer_isize] skewness: 0.560; kurtosis: 0.271; ap_prior: 7.05e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.61 sec [bwa_sai2sam_pe_core] changing coordinates of 1463 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7369 out of 8510 Q17 singletons are mated. [bwa_paired_sw] 89 out of 2716 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.98 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 786432 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 279) [infer_isize] low and high boundaries: 125 and 429 for estimating avg and std [infer_isize] inferred external isize from 193449 pairs: 241.079 +/- 54.501 [infer_isize] skewness: 0.551; kurtosis: 0.227; ap_prior: 1.42e-04 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.97 sec [bwa_sai2sam_pe_core] changing coordinates of 6994 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 25842 out of 27807 Q17 singletons are mated. [bwa_paired_sw] 3030 out of 12986 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 3.99 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.00 sec [bwa_sai2sam_pe_core] print alignments... 00:02:23.726 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:02:23.890 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
1.41 sec [bwa_sai2sam_pe_core] 1048576 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 279) [infer_isize] low and high boundaries: 125 and 429 for estimating avg and std [infer_isize] inferred external isize from 200644 pairs: 242.543 +/- 54.549 [infer_isize] skewness: 0.549; kurtosis: 0.240; ap_prior: 5.19e-05 [infer_isize] inferred maximum insert size: 621 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.78 sec [bwa_sai2sam_pe_core] changing coordinates of 11570 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8913 out of 9939 Q17 singletons are mated. [bwa_paired_sw] 567 out of 2654 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.19 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.02 sec [bwa_sai2sam_pe_core] print alignments... 1.47 sec [bwa_sai2sam_pe_core] 1310720 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 239159 pairs: 241.662 +/- 54.133 [infer_isize] skewness: 0.555; kurtosis: 0.271; ap_prior: 6.82e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.60 sec [bwa_sai2sam_pe_core] changing coordinates of 1707 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7599 out of 8778 Q17 singletons are mated. [bwa_paired_sw] 89 out of 2607 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.99 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.93 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 1572864 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 237, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 242340 pairs: 241.311 +/- 54.204 [infer_isize] skewness: 0.571; kurtosis: 0.276; ap_prior: 7.63e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) 00:03:24.787 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:03:24.900 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
[bwa_sai2sam_pe_core] time elapses: 7.90 sec [bwa_sai2sam_pe_core] changing coordinates of 1303 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 6817 out of 7968 Q17 singletons are mated. [bwa_paired_sw] 67 out of 2787 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.93 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec [bwa_sai2sam_pe_core] print alignments... 1.41 sec [bwa_sai2sam_pe_core] 1835008 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 241325 pairs: 242.727 +/- 53.973 [infer_isize] skewness: 0.532; kurtosis: 0.239; ap_prior: 5.15e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 5.75 sec [bwa_sai2sam_pe_core] changing coordinates of 1497 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7764 out of 8920 Q17 singletons are mated. [bwa_paired_sw] 48 out of 2150 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.98 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.82 sec [bwa_sai2sam_pe_core] print alignments... 1.41 sec [bwa_sai2sam_pe_core] 2097152 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 237866 pairs: 241.906 +/- 53.992 [infer_isize] skewness: 0.544; kurtosis: 0.246; ap_prior: 6.36e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.58 sec [bwa_sai2sam_pe_core] changing coordinates of 1856 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7057 out of 8173 Q17 singletons are mated. [bwa_paired_sw] 81 out of 2503 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.95 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.86 sec [bwa_sai2sam_pe_core] print alignments... 00:04:25.835 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:04:25.910 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
1.40 sec [bwa_sai2sam_pe_core] 2359296 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 236883 pairs: 241.639 +/- 54.175 [infer_isize] skewness: 0.556; kurtosis: 0.249; ap_prior: 6.79e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.89 sec [bwa_sai2sam_pe_core] changing coordinates of 2192 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8494 out of 9686 Q17 singletons are mated. [bwa_paired_sw] 149 out of 2672 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.07 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.01 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 2621440 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 238, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 239923 pairs: 242.138 +/- 54.082 [infer_isize] skewness: 0.543; kurtosis: 0.228; ap_prior: 6.51e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.19 sec [bwa_sai2sam_pe_core] changing coordinates of 865 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9328 out of 11155 Q17 singletons are mated. [bwa_paired_sw] 61 out of 2558 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.08 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec [bwa_sai2sam_pe_core] print alignments... 00:05:26.884 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:05:26.920 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
1.38 sec [bwa_sai2sam_pe_core] 2883584 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 241349 pairs: 241.734 +/- 54.166 [infer_isize] skewness: 0.555; kurtosis: 0.263; ap_prior: 6.91e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.43 sec [bwa_sai2sam_pe_core] changing coordinates of 1241 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8196 out of 9436 Q17 singletons are mated. [bwa_paired_sw] 48 out of 2547 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.03 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec [bwa_sai2sam_pe_core] print alignments... 1.38 sec [bwa_sai2sam_pe_core] 3145728 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 172352 pairs: 241.563 +/- 54.324 [infer_isize] skewness: 0.550; kurtosis: 0.239; ap_prior: 7.33e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.92 sec [bwa_sai2sam_pe_core] changing coordinates of 10130 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7724 out of 8696 Q17 singletons are mated. [bwa_paired_sw] 948 out of 3502 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.24 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.06 sec [bwa_sai2sam_pe_core] print alignments... 00:06:27.928 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:06:27.933 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
1.32 sec [bwa_sai2sam_pe_core] 3407872 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 222023 pairs: 241.686 +/- 54.293 [infer_isize] skewness: 0.553; kurtosis: 0.245; ap_prior: 7.01e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.25 sec [bwa_sai2sam_pe_core] changing coordinates of 5699 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7165 out of 8362 Q17 singletons are mated. [bwa_paired_sw] 216 out of 2754 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.98 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec [bwa_sai2sam_pe_core] print alignments... 1.42 sec [bwa_sai2sam_pe_core] 3670016 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 237, 277) [infer_isize] low and high boundaries: 125 and 423 for estimating avg and std [infer_isize] inferred external isize from 240218 pairs: 241.140 +/- 53.914 [infer_isize] skewness: 0.554; kurtosis: 0.242; ap_prior: 7.17e-05 [infer_isize] inferred maximum insert size: 615 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.64 sec [bwa_sai2sam_pe_core] changing coordinates of 1472 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7182 out of 8405 Q17 singletons are mated. [bwa_paired_sw] 99 out of 2734 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.95 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec [bwa_sai2sam_pe_core] print alignments... 00:07:28.942 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:07:28.960 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.41 sec [bwa_sai2sam_pe_core] 3932160 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 241089 pairs: 241.318 +/- 54.044 [infer_isize] skewness: 0.565; kurtosis: 0.273; ap_prior: 7.18e-05 [infer_isize] inferred maximum insert size: 616 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.18 sec [bwa_sai2sam_pe_core] changing coordinates of 1451 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7645 out of 8811 Q17 singletons are mated. [bwa_paired_sw] 100 out of 2706 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.98 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 4194304 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 238, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 237981 pairs: 242.180 +/- 54.232 [infer_isize] skewness: 0.549; kurtosis: 0.232; ap_prior: 6.82e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.26 sec [bwa_sai2sam_pe_core] changing coordinates of 2050 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8988 out of 10230 Q17 singletons are mated. [bwa_paired_sw] 158 out of 2672 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.10 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec [bwa_sai2sam_pe_core] print alignments... 00:08:29.953 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:08:30.008 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.39 sec [bwa_sai2sam_pe_core] 4456448 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 241952 pairs: 241.881 +/- 54.067 [infer_isize] skewness: 0.551; kurtosis: 0.257; ap_prior: 6.72e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.86 sec [bwa_sai2sam_pe_core] changing coordinates of 1268 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7525 out of 8753 Q17 singletons are mated. [bwa_paired_sw] 77 out of 2647 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.99 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.85 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 4718592 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 238, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 240858 pairs: 242.001 +/- 53.908 [infer_isize] skewness: 0.543; kurtosis: 0.239; ap_prior: 6.25e-05 [infer_isize] inferred maximum insert size: 616 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.24 sec [bwa_sai2sam_pe_core] changing coordinates of 1080 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8431 out of 9750 Q17 singletons are mated. [bwa_paired_sw] 114 out of 2579 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.06 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec [bwa_sai2sam_pe_core] print alignments... 00:09:30.963 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:09:31.051 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.40 sec [bwa_sai2sam_pe_core] 4980736 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (203, 237, 277) [infer_isize] low and high boundaries: 125 and 425 for estimating avg and std [infer_isize] inferred external isize from 240327 pairs: 241.033 +/- 54.127 [infer_isize] skewness: 0.565; kurtosis: 0.269; ap_prior: 7.44e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.75 sec [bwa_sai2sam_pe_core] changing coordinates of 1705 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 6876 out of 8054 Q17 singletons are mated. [bwa_paired_sw] 89 out of 2797 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.93 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 5242880 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 240821 pairs: 241.744 +/- 54.086 [infer_isize] skewness: 0.546; kurtosis: 0.236; ap_prior: 6.68e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.04 sec [bwa_sai2sam_pe_core] changing coordinates of 1832 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7051 out of 8278 Q17 singletons are mated. [bwa_paired_sw] 128 out of 2687 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.96 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.85 sec [bwa_sai2sam_pe_core] print alignments... 00:10:31.974 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:10:32.089 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.40 sec [bwa_sai2sam_pe_core] 5505024 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 238571 pairs: 241.322 +/- 54.103 [infer_isize] skewness: 0.561; kurtosis: 0.262; ap_prior: 6.96e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.82 sec [bwa_sai2sam_pe_core] changing coordinates of 1915 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8050 out of 9325 Q17 singletons are mated. [bwa_paired_sw] 156 out of 2792 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.03 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.93 sec [bwa_sai2sam_pe_core] print alignments... 1.41 sec [bwa_sai2sam_pe_core] 5767168 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 238, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 233693 pairs: 242.018 +/- 54.014 [infer_isize] skewness: 0.544; kurtosis: 0.226; ap_prior: 6.09e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.32 sec [bwa_sai2sam_pe_core] changing coordinates of 2837 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7822 out of 9072 Q17 singletons are mated. [bwa_paired_sw] 202 out of 2541 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.03 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 6029312 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... 00:11:32.984 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:11:33.115 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 193233 pairs: 241.293 +/- 54.170 [infer_isize] skewness: 0.569; kurtosis: 0.260; ap_prior: 8.38e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.76 sec [bwa_sai2sam_pe_core] changing coordinates of 1940 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7543 out of 8634 Q17 singletons are mated. [bwa_paired_sw] 263 out of 2722 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.05 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.83 sec [bwa_sai2sam_pe_core] print alignments... 1.21 sec [bwa_sai2sam_pe_core] 6291456 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 236541 pairs: 241.292 +/- 54.154 [infer_isize] skewness: 0.568; kurtosis: 0.269; ap_prior: 7.80e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.72 sec [bwa_sai2sam_pe_core] changing coordinates of 2010 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8347 out of 9632 Q17 singletons are mated. [bwa_paired_sw] 124 out of 3002 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.07 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.99 sec [bwa_sai2sam_pe_core] print alignments... 1.38 sec [bwa_sai2sam_pe_core] 6553600 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... 00:12:33.994 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:12:34.145 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [infer_isize] (25, 50, 75) percentile: (203, 237, 277) [infer_isize] low and high boundaries: 125 and 425 for estimating avg and std [infer_isize] inferred external isize from 239347 pairs: 240.791 +/- 54.158 [infer_isize] skewness: 0.576; kurtosis: 0.286; ap_prior: 7.98e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.77 sec [bwa_sai2sam_pe_core] changing coordinates of 2427 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 6503 out of 7723 Q17 singletons are mated. [bwa_paired_sw] 116 out of 2984 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.92 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 6815744 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 237, 277) [infer_isize] low and high boundaries: 125 and 423 for estimating avg and std [infer_isize] inferred external isize from 240281 pairs: 240.937 +/- 53.952 [infer_isize] skewness: 0.552; kurtosis: 0.235; ap_prior: 7.56e-05 [infer_isize] inferred maximum insert size: 615 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.27 sec [bwa_sai2sam_pe_core] changing coordinates of 2012 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 6640 out of 7894 Q17 singletons are mated. [bwa_paired_sw] 108 out of 2899 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.94 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 7077888 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... 00:13:35.004 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:13:35.177 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 239755 pairs: 241.239 +/- 54.064 [infer_isize] skewness: 0.559; kurtosis: 0.265; ap_prior: 7.83e-05 [infer_isize] inferred maximum insert size: 616 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.05 sec [bwa_sai2sam_pe_core] changing coordinates of 1549 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8247 out of 9546 Q17 singletons are mated. [bwa_paired_sw] 116 out of 2969 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.05 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.10 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 7340032 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 233124 pairs: 241.583 +/- 54.418 [infer_isize] skewness: 0.568; kurtosis: 0.257; ap_prior: 8.01e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.85 sec [bwa_sai2sam_pe_core] changing coordinates of 3221 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7800 out of 9095 Q17 singletons are mated. [bwa_paired_sw] 251 out of 3123 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.08 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 7602176 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 237, 277) [infer_isize] low and high boundaries: 125 and 423 for estimating avg and std [infer_isize] inferred external isize from 234349 pairs: 240.959 +/- 53.752 [infer_isize] skewness: 0.559; kurtosis: 0.261; ap_prior: 7.72e-05 [infer_isize] inferred maximum insert size: 614 (6.94 sigma) 00:14:36.013 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:14:36.214 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [bwa_sai2sam_pe_core] time elapses: 8.25 sec [bwa_sai2sam_pe_core] changing coordinates of 3343 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7231 out of 8437 Q17 singletons are mated. [bwa_paired_sw] 178 out of 2970 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.00 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 7864320 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 224990 pairs: 241.336 +/- 54.117 [infer_isize] skewness: 0.559; kurtosis: 0.265; ap_prior: 6.96e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.75 sec [bwa_sai2sam_pe_core] changing coordinates of 3464 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 6777 out of 7945 Q17 singletons are mated. [bwa_paired_sw] 106 out of 2651 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.93 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec [bwa_sai2sam_pe_core] print alignments... 1.41 sec [bwa_sai2sam_pe_core] 8126464 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (203, 237, 277) [infer_isize] low and high boundaries: 125 and 425 for estimating avg and std [infer_isize] inferred external isize from 239668 pairs: 240.865 +/- 54.172 [infer_isize] skewness: 0.570; kurtosis: 0.266; ap_prior: 8.10e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.54 sec [bwa_sai2sam_pe_core] changing coordinates of 2219 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7007 out of 8265 Q17 singletons are mated. [bwa_paired_sw] 105 out of 3048 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.97 sec [bwa_sai2sam_pe_core] refine gapped alignments... 00:15:37.023 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:15:37.243 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 0.86 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 8388608 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 237, 277) [infer_isize] low and high boundaries: 125 and 423 for estimating avg and std [infer_isize] inferred external isize from 240999 pairs: 240.997 +/- 54.002 [infer_isize] skewness: 0.548; kurtosis: 0.227; ap_prior: 7.84e-05 [infer_isize] inferred maximum insert size: 616 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.18 sec [bwa_sai2sam_pe_core] changing coordinates of 1584 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 6983 out of 8260 Q17 singletons are mated. [bwa_paired_sw] 105 out of 3003 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.95 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.86 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 8650752 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 238, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 241818 pairs: 242.106 +/- 53.944 [infer_isize] skewness: 0.538; kurtosis: 0.229; ap_prior: 5.80e-05 [infer_isize] inferred maximum insert size: 616 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.59 sec [bwa_sai2sam_pe_core] changing coordinates of 982 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8846 out of 10204 Q17 singletons are mated. [bwa_paired_sw] 169 out of 2541 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.04 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec [bwa_sai2sam_pe_core] print alignments... 00:16:38.035 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:16:38.334 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.40 sec [bwa_sai2sam_pe_core] 8912896 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 242516 pairs: 241.863 +/- 54.087 [infer_isize] skewness: 0.550; kurtosis: 0.243; ap_prior: 6.43e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.97 sec [bwa_sai2sam_pe_core] changing coordinates of 1028 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7618 out of 8924 Q17 singletons are mated. [bwa_paired_sw] 65 out of 2562 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.97 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 9175040 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 230394 pairs: 242.300 +/- 54.089 [infer_isize] skewness: 0.530; kurtosis: 0.193; ap_prior: 5.54e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.21 sec [bwa_sai2sam_pe_core] changing coordinates of 2970 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9675 out of 10954 Q17 singletons are mated. [bwa_paired_sw] 116 out of 2348 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.13 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.02 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 9437184 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... 00:17:39.046 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:17:39.370 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 239699 pairs: 241.969 +/- 54.184 [infer_isize] skewness: 0.565; kurtosis: 0.277; ap_prior: 6.32e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.66 sec [bwa_sai2sam_pe_core] changing coordinates of 1142 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9145 out of 10510 Q17 singletons are mated. [bwa_paired_sw] 83 out of 2524 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.08 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 9699328 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 238, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 241996 pairs: 242.065 +/- 53.988 [infer_isize] skewness: 0.539; kurtosis: 0.234; ap_prior: 6.31e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.72 sec [bwa_sai2sam_pe_core] changing coordinates of 952 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8374 out of 9615 Q17 singletons are mated. [bwa_paired_sw] 80 out of 2557 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.05 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 9961472 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (203, 237, 278) [infer_isize] low and high boundaries: 125 and 428 for estimating avg and std [infer_isize] inferred external isize from 234205 pairs: 240.975 +/- 54.236 [infer_isize] skewness: 0.581; kurtosis: 0.304; ap_prior: 1.08e-04 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) 00:18:40.056 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:18:40.402 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [bwa_sai2sam_pe_core] time elapses: 8.49 sec [bwa_sai2sam_pe_core] changing coordinates of 4314 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7508 out of 8772 Q17 singletons are mated. [bwa_paired_sw] 164 out of 3204 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.06 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 10223616 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 241409 pairs: 241.337 +/- 54.067 [infer_isize] skewness: 0.575; kurtosis: 0.292; ap_prior: 7.61e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.07 sec [bwa_sai2sam_pe_core] changing coordinates of 1593 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 6648 out of 7949 Q17 singletons are mated. [bwa_paired_sw] 86 out of 2921 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.92 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 10485760 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 242318 pairs: 241.163 +/- 54.208 [infer_isize] skewness: 0.565; kurtosis: 0.265; ap_prior: 7.16e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.26 sec [bwa_sai2sam_pe_core] changing coordinates of 1123 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7132 out of 8387 Q17 singletons are mated. [bwa_paired_sw] 61 out of 2758 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.95 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.85 sec [bwa_sai2sam_pe_core] print alignments... 00:19:41.066 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:19:41.431 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.40 sec [bwa_sai2sam_pe_core] 10747904 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 279) [infer_isize] low and high boundaries: 125 and 429 for estimating avg and std [infer_isize] inferred external isize from 232642 pairs: 242.107 +/- 54.538 [infer_isize] skewness: 0.559; kurtosis: 0.272; ap_prior: 8.50e-05 [infer_isize] inferred maximum insert size: 621 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.37 sec [bwa_sai2sam_pe_core] changing coordinates of 2939 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8947 out of 10345 Q17 singletons are mated. [bwa_paired_sw] 470 out of 2878 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.18 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 11010048 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 237944 pairs: 241.449 +/- 54.241 [infer_isize] skewness: 0.566; kurtosis: 0.256; ap_prior: 6.93e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.24 sec [bwa_sai2sam_pe_core] changing coordinates of 1803 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9422 out of 10715 Q17 singletons are mated. [bwa_paired_sw] 90 out of 2655 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.11 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec [bwa_sai2sam_pe_core] print alignments... 00:20:42.076 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:20:42.463 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.39 sec [bwa_sai2sam_pe_core] 11272192 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 241589 pairs: 241.877 +/- 54.100 [infer_isize] skewness: 0.554; kurtosis: 0.261; ap_prior: 6.48e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.86 sec [bwa_sai2sam_pe_core] changing coordinates of 1718 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7173 out of 8446 Q17 singletons are mated. [bwa_paired_sw] 97 out of 2664 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.98 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 11534336 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 280) [infer_isize] low and high boundaries: 125 and 432 for estimating avg and std [infer_isize] inferred external isize from 209044 pairs: 241.522 +/- 54.806 [infer_isize] skewness: 0.589; kurtosis: 0.332; ap_prior: 2.16e-04 [infer_isize] inferred maximum insert size: 622 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.25 sec [bwa_sai2sam_pe_core] changing coordinates of 9141 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7974 out of 9114 Q17 singletons are mated. [bwa_paired_sw] 2363 out of 5908 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.68 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.99 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 11796480 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 237, 277) [infer_isize] low and high boundaries: 125 and 423 for estimating avg and std [infer_isize] inferred external isize from 221239 pairs: 241.071 +/- 53.998 [infer_isize] skewness: 0.549; kurtosis: 0.224; ap_prior: 6.78e-05 [infer_isize] inferred maximum insert size: 616 (6.94 sigma) 00:21:43.087 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:21:43.488 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [bwa_sai2sam_pe_core] time elapses: 7.12 sec [bwa_sai2sam_pe_core] changing coordinates of 5527 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9036 out of 10330 Q17 singletons are mated. [bwa_paired_sw] 137 out of 2666 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.08 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.98 sec [bwa_sai2sam_pe_core] print alignments... 1.42 sec [bwa_sai2sam_pe_core] 12058624 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 218609 pairs: 241.787 +/- 54.166 [infer_isize] skewness: 0.555; kurtosis: 0.252; ap_prior: 7.90e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.84 sec [bwa_sai2sam_pe_core] changing coordinates of 4611 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 10112 out of 11387 Q17 singletons are mated. [bwa_paired_sw] 126 out of 2491 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.18 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.05 sec [bwa_sai2sam_pe_core] print alignments... 1.42 sec [bwa_sai2sam_pe_core] 12320768 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 237, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 242319 pairs: 241.220 +/- 54.138 [infer_isize] skewness: 0.564; kurtosis: 0.266; ap_prior: 7.51e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.75 sec [bwa_sai2sam_pe_core] changing coordinates of 1436 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 6544 out of 7804 Q17 singletons are mated. [bwa_paired_sw] 86 out of 2933 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.91 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec [bwa_sai2sam_pe_core] print alignments... 00:22:44.097 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:22:44.515 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.39 sec [bwa_sai2sam_pe_core] 12582912 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 232523 pairs: 241.792 +/- 54.116 [infer_isize] skewness: 0.550; kurtosis: 0.239; ap_prior: 6.30e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.38 sec [bwa_sai2sam_pe_core] changing coordinates of 2633 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9185 out of 10503 Q17 singletons are mated. [bwa_paired_sw] 129 out of 2574 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.10 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 12845056 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 232904 pairs: 242.020 +/- 54.229 [infer_isize] skewness: 0.549; kurtosis: 0.242; ap_prior: 6.33e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.51 sec [bwa_sai2sam_pe_core] changing coordinates of 3660 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9223 out of 10590 Q17 singletons are mated. [bwa_paired_sw] 188 out of 2627 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.15 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.01 sec [bwa_sai2sam_pe_core] print alignments... 1.41 sec [bwa_sai2sam_pe_core] 13107200 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... 00:23:45.108 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:23:45.545 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 219802 pairs: 241.772 +/- 54.243 [infer_isize] skewness: 0.566; kurtosis: 0.258; ap_prior: 7.47e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 10.74 sec [bwa_sai2sam_pe_core] changing coordinates of 3894 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7542 out of 8921 Q17 singletons are mated. [bwa_paired_sw] 172 out of 2869 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.00 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.81 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 13369344 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 217339 pairs: 241.578 +/- 54.285 [infer_isize] skewness: 0.561; kurtosis: 0.269; ap_prior: 7.24e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 9.32 sec [bwa_sai2sam_pe_core] changing coordinates of 5582 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7345 out of 8649 Q17 singletons are mated. [bwa_paired_sw] 402 out of 3103 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.04 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.97 sec [bwa_sai2sam_pe_core] print alignments... 00:24:46.118 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:24:46.576 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.44 sec [bwa_sai2sam_pe_core] 13631488 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 207599 pairs: 241.946 +/- 54.334 [infer_isize] skewness: 0.557; kurtosis: 0.251; ap_prior: 6.88e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.03 sec [bwa_sai2sam_pe_core] changing coordinates of 2486 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7069 out of 8259 Q17 singletons are mated. [bwa_paired_sw] 123 out of 2524 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.96 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec [bwa_sai2sam_pe_core] print alignments... 1.29 sec [bwa_sai2sam_pe_core] 13893632 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 237102 pairs: 241.269 +/- 54.105 [infer_isize] skewness: 0.558; kurtosis: 0.271; ap_prior: 7.43e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.94 sec [bwa_sai2sam_pe_core] changing coordinates of 1746 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7152 out of 8466 Q17 singletons are mated. [bwa_paired_sw] 95 out of 2884 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.95 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.86 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 14155776 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. 00:25:47.127 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
[bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... 00:25:47.602 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 241742 pairs: 241.442 +/- 54.195 [infer_isize] skewness: 0.565; kurtosis: 0.269; ap_prior: 7.46e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.97 sec [bwa_sai2sam_pe_core] changing coordinates of 1357 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 6962 out of 8292 Q17 singletons are mated. [bwa_paired_sw] 91 out of 2910 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.96 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.93 sec [bwa_sai2sam_pe_core] print alignments... 1.42 sec [bwa_sai2sam_pe_core] 14417920 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 237545 pairs: 242.005 +/- 54.241 [infer_isize] skewness: 0.546; kurtosis: 0.234; ap_prior: 6.70e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.27 sec [bwa_sai2sam_pe_core] changing coordinates of 1859 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7586 out of 8886 Q17 singletons are mated. [bwa_paired_sw] 176 out of 2795 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.01 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec [bwa_sai2sam_pe_core] print alignments... 1.41 sec [bwa_sai2sam_pe_core] 14680064 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... 00:26:48.136 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:26:48.642 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 165910 pairs: 241.445 +/- 54.164 [infer_isize] skewness: 0.556; kurtosis: 0.255; ap_prior: 6.87e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.99 sec [bwa_sai2sam_pe_core] changing coordinates of 10492 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 6833 out of 7929 Q17 singletons are mated. [bwa_paired_sw] 575 out of 2957 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.06 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.05 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 14942208 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 239475 pairs: 241.925 +/- 54.169 [infer_isize] skewness: 0.550; kurtosis: 0.242; ap_prior: 6.71e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.42 sec [bwa_sai2sam_pe_core] changing coordinates of 1769 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7245 out of 8509 Q17 singletons are mated. [bwa_paired_sw] 57 out of 2667 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.96 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.83 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 15204352 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 236985 pairs: 242.755 +/- 54.228 [infer_isize] skewness: 0.538; kurtosis: 0.221; ap_prior: 5.33e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.23 sec [bwa_sai2sam_pe_core] changing coordinates of 1542 alignments. [bwa_sai2sam_pe_core] align unmapped mate... 00:27:49.147 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:27:49.666 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [bwa_paired_sw] 9598 out of 10961 Q17 singletons are mated. [bwa_paired_sw] 205 out of 2501 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.17 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec [bwa_sai2sam_pe_core] print alignments... 1.41 sec [bwa_sai2sam_pe_core] 15466496 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 240, 283) [infer_isize] low and high boundaries: 125 and 439 for estimating avg and std [infer_isize] inferred external isize from 164815 pairs: 241.293 +/- 54.960 [infer_isize] skewness: 0.609; kurtosis: 0.423; ap_prior: 4.07e-04 [infer_isize] inferred maximum insert size: 623 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.31 sec [bwa_sai2sam_pe_core] changing coordinates of 11751 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 16477 out of 17913 Q17 singletons are mated. [bwa_paired_sw] 6646 out of 14896 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 3.94 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.29 sec [bwa_sai2sam_pe_core] print alignments... 1.31 sec [bwa_sai2sam_pe_core] 15728640 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 279) [infer_isize] low and high boundaries: 125 and 429 for estimating avg and std [infer_isize] inferred external isize from 180808 pairs: 241.650 +/- 54.397 [infer_isize] skewness: 0.570; kurtosis: 0.289; ap_prior: 1.18e-04 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.54 sec [bwa_sai2sam_pe_core] changing coordinates of 8446 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 18848 out of 20965 Q17 singletons are mated. [bwa_paired_sw] 2413 out of 7478 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 2.75 sec [bwa_sai2sam_pe_core] refine gapped alignments... 00:28:50.156 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
1.03 sec [bwa_sai2sam_pe_core] print alignments... 00:28:50.699 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.38 sec [bwa_sai2sam_pe_core] 15990784 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 238, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 237342 pairs: 242.157 +/- 53.980 [infer_isize] skewness: 0.544; kurtosis: 0.236; ap_prior: 5.96e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.93 sec [bwa_sai2sam_pe_core] changing coordinates of 2125 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8926 out of 10371 Q17 singletons are mated. [bwa_paired_sw] 83 out of 2468 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.07 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec [bwa_sai2sam_pe_core] print alignments... 1.41 sec [bwa_sai2sam_pe_core] 16252928 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 236010 pairs: 242.648 +/- 54.404 [infer_isize] skewness: 0.550; kurtosis: 0.248; ap_prior: 6.07e-05 [infer_isize] inferred maximum insert size: 620 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.92 sec [bwa_sai2sam_pe_core] changing coordinates of 1412 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8689 out of 10138 Q17 singletons are mated. [bwa_paired_sw] 146 out of 2542 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.09 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec [bwa_sai2sam_pe_core] print alignments... 00:29:51.165 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:29:51.802 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.39 sec [bwa_sai2sam_pe_core] 16515072 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 239670 pairs: 241.812 +/- 54.151 [infer_isize] skewness: 0.553; kurtosis: 0.237; ap_prior: 7.06e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.94 sec [bwa_sai2sam_pe_core] changing coordinates of 1772 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7567 out of 8903 Q17 singletons are mated. [bwa_paired_sw] 119 out of 2821 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.00 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 16777216 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 222796 pairs: 242.972 +/- 54.182 [infer_isize] skewness: 0.540; kurtosis: 0.222; ap_prior: 5.34e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.45 sec [bwa_sai2sam_pe_core] changing coordinates of 1866 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9087 out of 10416 Q17 singletons are mated. [bwa_paired_sw] 179 out of 2372 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.11 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec [bwa_sai2sam_pe_core] print alignments... 1.35 sec [bwa_sai2sam_pe_core] 17039360 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... 00:30:52.175 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:30:52.830 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 238431 pairs: 241.573 +/- 54.091 [infer_isize] skewness: 0.561; kurtosis: 0.274; ap_prior: 6.92e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.26 sec [bwa_sai2sam_pe_core] changing coordinates of 2225 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7661 out of 9041 Q17 singletons are mated. [bwa_paired_sw] 100 out of 2855 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.00 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 17301504 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 238517 pairs: 242.691 +/- 54.200 [infer_isize] skewness: 0.534; kurtosis: 0.215; ap_prior: 5.24e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.15 sec [bwa_sai2sam_pe_core] changing coordinates of 1554 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9296 out of 10655 Q17 singletons are mated. [bwa_paired_sw] 75 out of 2253 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.09 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec [bwa_sai2sam_pe_core] print alignments... 1.41 sec [bwa_sai2sam_pe_core] 17563648 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 239624 pairs: 241.711 +/- 54.205 [infer_isize] skewness: 0.566; kurtosis: 0.267; ap_prior: 7.25e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) 00:31:53.186 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:31:53.867 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [bwa_sai2sam_pe_core] time elapses: 6.91 sec [bwa_sai2sam_pe_core] changing coordinates of 1734 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8306 out of 9642 Q17 singletons are mated. [bwa_paired_sw] 199 out of 2983 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.08 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.06 sec [bwa_sai2sam_pe_core] print alignments... 1.42 sec [bwa_sai2sam_pe_core] 17825792 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 236157 pairs: 242.325 +/- 54.285 [infer_isize] skewness: 0.543; kurtosis: 0.234; ap_prior: 5.99e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.91 sec [bwa_sai2sam_pe_core] changing coordinates of 1344 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9037 out of 10480 Q17 singletons are mated. [bwa_paired_sw] 170 out of 2642 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.11 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec [bwa_sai2sam_pe_core] print alignments... 1.37 sec [bwa_sai2sam_pe_core] 18087936 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 238149 pairs: 241.347 +/- 54.168 [infer_isize] skewness: 0.565; kurtosis: 0.271; ap_prior: 6.74e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 8.20 sec [bwa_sai2sam_pe_core] changing coordinates of 1932 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8677 out of 10299 Q17 singletons are mated. [bwa_paired_sw] 164 out of 2811 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.05 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.93 sec [bwa_sai2sam_pe_core] print alignments... 00:32:54.197 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:32:54.891 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.38 sec [bwa_sai2sam_pe_core] 18350080 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 241676 pairs: 241.561 +/- 54.104 [infer_isize] skewness: 0.559; kurtosis: 0.266; ap_prior: 6.62e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.32 sec [bwa_sai2sam_pe_core] changing coordinates of 1170 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7904 out of 9180 Q17 singletons are mated. [bwa_paired_sw] 65 out of 2708 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.00 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 18612224 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 237795 pairs: 242.306 +/- 54.049 [infer_isize] skewness: 0.536; kurtosis: 0.207; ap_prior: 6.24e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.11 sec [bwa_sai2sam_pe_core] changing coordinates of 1420 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 10665 out of 12145 Q17 singletons are mated. [bwa_paired_sw] 138 out of 2651 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.21 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec [bwa_sai2sam_pe_core] print alignments... 00:33:55.207 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:33:55.932 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.40 sec [bwa_sai2sam_pe_core] 18874368 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 240122 pairs: 241.747 +/- 54.155 [infer_isize] skewness: 0.560; kurtosis: 0.270; ap_prior: 6.81e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.03 sec [bwa_sai2sam_pe_core] changing coordinates of 1405 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8267 out of 9643 Q17 singletons are mated. [bwa_paired_sw] 100 out of 2824 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.04 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.01 sec [bwa_sai2sam_pe_core] print alignments... 1.38 sec [bwa_sai2sam_pe_core] 19136512 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 237, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 238939 pairs: 241.117 +/- 54.132 [infer_isize] skewness: 0.572; kurtosis: 0.292; ap_prior: 7.93e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.52 sec [bwa_sai2sam_pe_core] changing coordinates of 1734 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7713 out of 9032 Q17 singletons are mated. [bwa_paired_sw] 112 out of 3134 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.01 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec [bwa_sai2sam_pe_core] print alignments... 1.38 sec [bwa_sai2sam_pe_core] 19398656 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... 00:34:56.217 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:34:56.970 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [infer_isize] (25, 50, 75) percentile: (204, 237, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 241223 pairs: 241.199 +/- 54.272 [infer_isize] skewness: 0.576; kurtosis: 0.288; ap_prior: 8.00e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.70 sec [bwa_sai2sam_pe_core] changing coordinates of 1145 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7723 out of 9021 Q17 singletons are mated. [bwa_paired_sw] 75 out of 3055 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.01 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.00 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 19660800 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 228855 pairs: 241.991 +/- 54.371 [infer_isize] skewness: 0.560; kurtosis: 0.262; ap_prior: 7.11e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.40 sec [bwa_sai2sam_pe_core] changing coordinates of 3584 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8220 out of 9625 Q17 singletons are mated. [bwa_paired_sw] 203 out of 2908 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.07 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.06 sec [bwa_sai2sam_pe_core] print alignments... 1.41 sec [bwa_sai2sam_pe_core] 19922944 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 239673 pairs: 241.343 +/- 54.120 [infer_isize] skewness: 0.559; kurtosis: 0.268; ap_prior: 7.46e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) 00:35:57.227 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:35:58.013 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [bwa_sai2sam_pe_core] time elapses: 8.23 sec [bwa_sai2sam_pe_core] changing coordinates of 1652 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 7887 out of 9252 Q17 singletons are mated. [bwa_paired_sw] 95 out of 3074 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.03 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec [bwa_sai2sam_pe_core] print alignments... 1.38 sec [bwa_sai2sam_pe_core] 20185088 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 238, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 241111 pairs: 241.994 +/- 53.964 [infer_isize] skewness: 0.550; kurtosis: 0.235; ap_prior: 6.18e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.63 sec [bwa_sai2sam_pe_core] changing coordinates of 811 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8984 out of 10444 Q17 singletons are mated. [bwa_paired_sw] 70 out of 2524 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.06 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 20447232 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 241787 pairs: 242.718 +/- 54.491 [infer_isize] skewness: 0.548; kurtosis: 0.238; ap_prior: 5.57e-05 [infer_isize] inferred maximum insert size: 621 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.12 sec [bwa_sai2sam_pe_core] changing coordinates of 560 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9140 out of 10732 Q17 singletons are mated. [bwa_paired_sw] 39 out of 2368 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.08 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec [bwa_sai2sam_pe_core] print alignments... 00:36:58.237 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:36:59.037 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.40 sec [bwa_sai2sam_pe_core] 20709376 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 211208 pairs: 241.952 +/- 54.254 [infer_isize] skewness: 0.550; kurtosis: 0.245; ap_prior: 7.35e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.26 sec [bwa_sai2sam_pe_core] changing coordinates of 6941 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9654 out of 11048 Q17 singletons are mated. [bwa_paired_sw] 713 out of 3672 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.34 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.02 sec [bwa_sai2sam_pe_core] print alignments... 1.44 sec [bwa_sai2sam_pe_core] 20971520 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 238, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 232720 pairs: 242.181 +/- 54.097 [infer_isize] skewness: 0.537; kurtosis: 0.208; ap_prior: 5.86e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.92 sec [bwa_sai2sam_pe_core] changing coordinates of 2321 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8616 out of 10046 Q17 singletons are mated. [bwa_paired_sw] 227 out of 2662 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.08 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec [bwa_sai2sam_pe_core] print alignments... 00:37:59.248 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:38:00.064 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.41 sec [bwa_sai2sam_pe_core] 21233664 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 230618 pairs: 242.563 +/- 54.232 [infer_isize] skewness: 0.542; kurtosis: 0.236; ap_prior: 5.70e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.50 sec [bwa_sai2sam_pe_core] changing coordinates of 3391 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9369 out of 10877 Q17 singletons are mated. [bwa_paired_sw] 164 out of 2452 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.13 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 21495808 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 239, 280) [infer_isize] low and high boundaries: 125 and 432 for estimating avg and std [infer_isize] inferred external isize from 175886 pairs: 242.093 +/- 54.809 [infer_isize] skewness: 0.575; kurtosis: 0.310; ap_prior: 1.50e-04 [infer_isize] inferred maximum insert size: 622 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.88 sec [bwa_sai2sam_pe_core] changing coordinates of 14849 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 10410 out of 11647 Q17 singletons are mated. [bwa_paired_sw] 1098 out of 3950 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.53 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.98 sec [bwa_sai2sam_pe_core] print alignments... 1.45 sec [bwa_sai2sam_pe_core] 21757952 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... 00:39:00.260 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:39:01.108 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [infer_isize] (25, 50, 75) percentile: (205, 238, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 240042 pairs: 242.133 +/- 53.974 [infer_isize] skewness: 0.538; kurtosis: 0.219; ap_prior: 6.07e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.88 sec [bwa_sai2sam_pe_core] changing coordinates of 1189 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8823 out of 10263 Q17 singletons are mated. [bwa_paired_sw] 59 out of 2533 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.06 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 22020096 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 235826 pairs: 243.120 +/- 54.317 [infer_isize] skewness: 0.533; kurtosis: 0.212; ap_prior: 4.75e-05 [infer_isize] inferred maximum insert size: 620 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 5.85 sec [bwa_sai2sam_pe_core] changing coordinates of 1184 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 11886 out of 13477 Q17 singletons are mated. [bwa_paired_sw] 144 out of 2219 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.29 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.00 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 22282240 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 239, 279) [infer_isize] low and high boundaries: 125 and 429 for estimating avg and std [infer_isize] inferred external isize from 203989 pairs: 242.361 +/- 54.435 [infer_isize] skewness: 0.557; kurtosis: 0.255; ap_prior: 6.65e-05 [infer_isize] inferred maximum insert size: 620 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 5.81 sec [bwa_sai2sam_pe_core] changing coordinates of 5352 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 11501 out of 13005 Q17 singletons are mated. [bwa_paired_sw] 500 out of 3014 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.39 sec [bwa_sai2sam_pe_core] refine gapped alignments... 00:40:01.269 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
0.90 sec [bwa_sai2sam_pe_core] print alignments... 00:40:02.136 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.38 sec [bwa_sai2sam_pe_core] 22544384 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 234558 pairs: 242.925 +/- 54.183 [infer_isize] skewness: 0.536; kurtosis: 0.228; ap_prior: 4.77e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 5.40 sec [bwa_sai2sam_pe_core] changing coordinates of 2309 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 10097 out of 11556 Q17 singletons are mated. [bwa_paired_sw] 77 out of 2200 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.14 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 22806528 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 238, 278) [infer_isize] low and high boundaries: 125 and 424 for estimating avg and std [infer_isize] inferred external isize from 238233 pairs: 242.014 +/- 54.015 [infer_isize] skewness: 0.546; kurtosis: 0.231; ap_prior: 6.17e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.16 sec [bwa_sai2sam_pe_core] changing coordinates of 1779 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9106 out of 10609 Q17 singletons are mated. [bwa_paired_sw] 112 out of 2578 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.09 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 23068672 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... 00:41:02.279 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:41:03.163 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 232179 pairs: 243.228 +/- 54.536 [infer_isize] skewness: 0.531; kurtosis: 0.197; ap_prior: 4.67e-05 [infer_isize] inferred maximum insert size: 622 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 5.63 sec [bwa_sai2sam_pe_core] changing coordinates of 1424 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 12265 out of 13789 Q17 singletons are mated. [bwa_paired_sw] 233 out of 2436 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.42 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec [bwa_sai2sam_pe_core] print alignments... 1.38 sec [bwa_sai2sam_pe_core] 23330816 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 221149 pairs: 241.475 +/- 54.270 [infer_isize] skewness: 0.571; kurtosis: 0.276; ap_prior: 7.39e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.19 sec [bwa_sai2sam_pe_core] changing coordinates of 2589 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 9311 out of 10672 Q17 singletons are mated. [bwa_paired_sw] 223 out of 2908 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.14 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.89 sec [bwa_sai2sam_pe_core] print alignments... 1.35 sec [bwa_sai2sam_pe_core] 23592960 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 241875 pairs: 241.740 +/- 54.114 [infer_isize] skewness: 0.550; kurtosis: 0.239; ap_prior: 6.90e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.21 sec [bwa_sai2sam_pe_core] changing coordinates of 1003 alignments. [bwa_sai2sam_pe_core] align unmapped mate... 00:42:03.289 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:42:04.192 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [bwa_paired_sw] 7307 out of 8701 Q17 singletons are mated. [bwa_paired_sw] 65 out of 2842 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.96 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.89 sec [bwa_sai2sam_pe_core] print alignments... 1.41 sec [bwa_sai2sam_pe_core] 23855104 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 240216 pairs: 241.660 +/- 54.105 [infer_isize] skewness: 0.560; kurtosis: 0.269; ap_prior: 7.01e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 7.22 sec [bwa_sai2sam_pe_core] changing coordinates of 979 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8792 out of 10260 Q17 singletons are mated. [bwa_paired_sw] 121 out of 2866 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.09 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec [bwa_sai2sam_pe_core] print alignments... 1.38 sec [bwa_sai2sam_pe_core] 24117248 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 234765 pairs: 242.776 +/- 54.312 [infer_isize] skewness: 0.551; kurtosis: 0.245; ap_prior: 5.67e-05 [infer_isize] inferred maximum insert size: 620 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.45 sec [bwa_sai2sam_pe_core] changing coordinates of 1428 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8458 out of 9917 Q17 singletons are mated. [bwa_paired_sw] 229 out of 2699 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.09 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.85 sec [bwa_sai2sam_pe_core] print alignments... 00:43:04.300 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:43:05.218 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.38 sec [bwa_sai2sam_pe_core] 24379392 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 194632 pairs: 242.906 +/- 54.133 [infer_isize] skewness: 0.542; kurtosis: 0.248; ap_prior: 5.47e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 5.82 sec [bwa_sai2sam_pe_core] changing coordinates of 1837 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 11734 out of 13338 Q17 singletons are mated. [bwa_paired_sw] 319 out of 2430 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.34 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec [bwa_sai2sam_pe_core] print alignments... 1.25 sec [bwa_sai2sam_pe_core] 24641536 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (206, 239, 279) [infer_isize] low and high boundaries: 125 and 425 for estimating avg and std [infer_isize] inferred external isize from 235487 pairs: 243.090 +/- 54.007 [infer_isize] skewness: 0.518; kurtosis: 0.189; ap_prior: 4.67e-05 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 5.25 sec [bwa_sai2sam_pe_core] changing coordinates of 688 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 14407 out of 16066 Q17 singletons are mated. [bwa_paired_sw] 38 out of 2101 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.42 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec [bwa_sai2sam_pe_core] print alignments... 1.39 sec [bwa_sai2sam_pe_core] 24903680 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... 00:44:05.311 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:44:06.242 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 209885 pairs: 242.759 +/- 54.445 [infer_isize] skewness: 0.542; kurtosis: 0.225; ap_prior: 7.64e-05 [infer_isize] inferred maximum insert size: 621 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.09 sec [bwa_sai2sam_pe_core] changing coordinates of 2187 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 18103 out of 20206 Q17 singletons are mated. [bwa_paired_sw] 1580 out of 8401 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 2.68 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.97 sec [bwa_sai2sam_pe_core] print alignments... 1.37 sec [bwa_sai2sam_pe_core] 25165824 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 214545 pairs: 242.922 +/- 54.190 [infer_isize] skewness: 0.531; kurtosis: 0.219; ap_prior: 5.74e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 5.82 sec [bwa_sai2sam_pe_core] changing coordinates of 7312 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 12477 out of 14025 Q17 singletons are mated. [bwa_paired_sw] 202 out of 2278 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.33 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.98 sec [bwa_sai2sam_pe_core] print alignments... 1.40 sec [bwa_sai2sam_pe_core] 25427968 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 224301 pairs: 242.907 +/- 54.135 [infer_isize] skewness: 0.531; kurtosis: 0.218; ap_prior: 6.02e-05 [infer_isize] inferred maximum insert size: 619 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.06 sec [bwa_sai2sam_pe_core] changing coordinates of 4498 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 8901 out of 10339 Q17 singletons are mated. [bwa_paired_sw] 313 out of 2657 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.13 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec [bwa_sai2sam_pe_core] print alignments... 00:45:06.323 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:45:07.272 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.41 sec [bwa_sai2sam_pe_core] 25690112 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (204, 238, 278) [infer_isize] low and high boundaries: 125 and 426 for estimating avg and std [infer_isize] inferred external isize from 217409 pairs: 241.736 +/- 54.137 [infer_isize] skewness: 0.557; kurtosis: 0.261; ap_prior: 6.86e-05 [infer_isize] inferred maximum insert size: 617 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 6.65 sec [bwa_sai2sam_pe_core] changing coordinates of 3923 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 11035 out of 12609 Q17 singletons are mated. [bwa_paired_sw] 474 out of 3372 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.38 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.16 sec [bwa_sai2sam_pe_core] print alignments... 1.36 sec [bwa_sai2sam_pe_core] 25952256 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (205, 239, 279) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 131869 pairs: 242.488 +/- 54.584 [infer_isize] skewness: 0.540; kurtosis: 0.220; ap_prior: 7.70e-05 [infer_isize] inferred maximum insert size: 621 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 5.40 sec [bwa_sai2sam_pe_core] changing coordinates of 5325 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 14489 out of 15932 Q17 singletons are mated. [bwa_paired_sw] 1142 out of 3588 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.88 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.05 sec [bwa_sai2sam_pe_core] print alignments... 00:46:07.333 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:46:08.299 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 1.08 sec [bwa_sai2sam_pe_core] 26214400 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (199, 234, 275) [infer_isize] low and high boundaries: 125 and 427 for estimating avg and std [infer_isize] inferred external isize from 15370 pairs: 237.628 +/- 54.847 [infer_isize] skewness: 0.570; kurtosis: 0.230; ap_prior: 1.33e-04 [infer_isize] inferred maximum insert size: 618 (6.94 sigma) [bwa_sai2sam_pe_core] time elapses: 3.06 sec [bwa_sai2sam_pe_core] changing coordinates of 4990 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 10195 out of 12365 Q17 singletons are mated. [bwa_paired_sw] 1265 out of 2897 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 1.52 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.57 sec [bwa_sai2sam_pe_core] print alignments... 0.59 sec [bwa_sai2sam_pe_core] 26458520 sequences have been processed. [main] Version: 0.7.13-r1126 [main] CMD: bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.sai ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq [main] Real time: 2762.464 sec; CPU: 1156.834 sec 00:47:08.341 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:47:09.323 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:48:09.350 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:48:10.347 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:49:10.359 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:49:11.376 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:50:11.367 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:50:12.410 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:51:12.376 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:51:13.435 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:52:13.385 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:52:14.460 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:53:14.394 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:53:15.486 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:54:15.402 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:54:16.513 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:55:16.410 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:55:17.545 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:56:17.418 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:56:18.568 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:57:18.426 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:57:19.608 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:58:19.435 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:58:20.633 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 00:59:20.443 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
00:59:21.656 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:00:21.451 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:00:22.684 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:01:22.459 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:01:23.708 Writing report file 'chipseq.bds.20170602_104615_132.report.html' [bam_sort_core] merging from 39 files... 01:02:23.467 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:02:24.730 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:03:24.474 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:03:25.752 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:04:25.483 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:04:26.783 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:05:26.491 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:05:27.807 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:06:27.498 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:06:28.832 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:07:28.505 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:07:29.856 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:08:29.513 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:08:30.878 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:09:30.521 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:09:31.899 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:10:31.529 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:10:32.922 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:11:32.537 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:11:33.946 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:12:33.546 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:12:34.972 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:13:34.554 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:13:35.996 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:14:35.562 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:14:37.060 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:15:36.571 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0 PID Task state Task name Dependencies Task definition
15573 running (RUNNING) bwa_sam_PE rep1 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re
01:15:38.087 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:15:48.610 Wait: Task 'chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' finished. 01:15:48.615 Wait: Waiting for task to finish: chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10, state: FINISHED 01:15:48.615 Wait: Task 'chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' finished. 01:15:48.617 Wait: Waiting for task to finish: chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10, state: FINISHED 01:15:48.617 Wait: Task 'chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' finished. 01:15:49.799 ExecutionerLocal 'Local[38]': Queuing task: chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11 01:15:49.799 Waiting for all tasks to finish. 01:15:49.800 Wait: Waiting for task to finish: chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10, state: FINISHED 01:15:49.800 Wait: Task 'chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' finished. 01:15:49.800 Wait: Waiting for task to finish: chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11, state: SCHEDULED 01:15:50.075 ExecutionerLocal 'Local[38]': Task selected 'chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11' on host 'localhost' 01:16:37.590 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 1 Failed: 0 PID Task state Task name Dependencies Task definition
16002 running (RUNNING) dedup_bam_PE_1 rep1 if [[ 0 > 0 ]]; then; samtools view -F 524 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam ; sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI
01:16:39.322 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:17:38.614 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 1 Failed: 0 PID Task state Task name Dependencies Task definition
16002 running (RUNNING) dedup_bam_PE_1 rep1 if [[ 0 > 0 ]]; then; samtools view -F 524 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam ; sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI

01:17:40.431 Writing report file 'chipseq.bds.20170602_104615_132.report.html' sambamba-sort: Unable to write to stream ChIPSeq/chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11.sh: line 21: 19368 Broken pipe samtools view -F 1804 -f 2 -q 30 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam 19369 Segmentation fault (core dumped) | sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam Task failed: Program & line : 'tools/TF_chipseq_pipeline/modules/postalign_bam.bds', line 260 Task Name : 'dedup_bam_PE_1 rep1' Task ID : 'chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11' Task PID : '16002' Task hint : 'if [[ 0 > 0 ]]; then; samtools view -F 524 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam |; sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI' Task resources : 'cpus: -1 mem: -1.0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam]' Output files : '[ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.filt.bam]' Script file : 'ChIPSeq/chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11.sh' Exit status : '1' Program : 

    # SYS command. line 262

     if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

    # SYS command. line 278

     if [[ 0 > 0 ]]; then \
                    samtools view -F 524 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam | \
                    sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam; \
                    samtools view -h ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam | \
                    $(which assign_multimappers.py) -k 0 --paired-end | \
                    samtools fixmate -r /dev/stdin ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam.fixmate.bam; \
                    else \
                        samtools view -F 1804 -f 2 -q 30 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam | \
                        sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam; \
                        samtools fixmate -r ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam.fixmate.bam; \
                    fi

    # SYS command. line 290

     samtools view -F 1804 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam.fixmate.bam | sambamba sort -t 1 /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.filt.bam

    # SYS command. line 292

     rm -f ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam.fixmate.bam

    # SYS command. line 293

     rm -f ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam

    # SYS command. line 295

     TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
StdErr (100000000 lines)  :
    sambamba-sort: Unable to write to stream
    ChIPSeq/chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11.sh: line 21: 19368 Broken pipe             samtools view -F 1804 -f 2 -q 30 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam
         19369 Segmentation fault      (core dumped) | sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam

01:17:55.737 Wait: Task 'chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11' finished. Fatal error: tools/TF_chipseq_pipeline/modules/postalign_bam.bds, line 300, pos 3. Task/s failed. chipseq.bds, line 76 : main() chipseq.bds, line 79 : void main() { // chipseq pipeline starts here chipseq.bds, line 87 : align() // align and postalign chipseq.bds, line 318 : void align() { chipseq.bds, line 355 : for ( int ctl=0; ctl <= 1; ctl++) { // iterate through inputs (ctl==0 : exp. replicate, ctl==1 : control) chipseq.bds, line 358 : for ( int rep=1; rep <= get_num_rep( ctl ); rep++) { chipseq.bds, line 364 : if ( no_par ) align( ctl, rep, nth_rep{group} ) // parallel jobs for align() for each replicate and each control chipseq.bds, line 374 : void align( int ctl, int rep, int nth_rep ) { chipseq.bds, line 376 : if ( is_se( ctl, rep ) ) align_SE( ctl, rep, nth_rep ) chipseq.bds, line 377 : else align_PE( ctl, rep, nth_rep ) chipseq.bds, line 550 : void align_PE( int ctl, int rep, int nth_rep ) { chipseq.bds, line 624 : if ( is_input_bam( ctl, rep ) || is_input_fastq( ctl, rep ) ) { chipseq.bds, line 633 : if ( no_dup_removal ) { chipseq.bds, line 637 : else { chipseq.bds, line 638 : ( filtbam, dupqc, flagstat_nodupqc, pbcqc ) \ chipseq.bds, line 639 : = dedup_bamPE( bam, aln_o_dir, qc_o_dir, group, nth_rep )
postalign_bam.bds, line 233 : string[] dedup_bam_PE( string bam, string o_dir, string log_o_dir, string group, int nth_dedup ) { postalign_bam.bds, line 249 : if ( out<-in ) { postalign_bam.bds, line 300 : wait

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. 01:17:55.894 Writing report file 'chipseq.bds.20170602_104615_132.report.html' 01:17:55.935 Program 'chipseq.bds.20170602_104615_132' finished, exit value: 1, tasks executed: 2, tasks failed: 1, tasks failed names: dedup_bam_PE_1 rep1. 01:17:55.935 Finished. Exit code: 1 01:17:55.935 ExecutionerLocal 'Local[38]': Killed

rdali commented 7 years ago

################################### STDOUT of ChIPSeq pipeline ################################### ################################### STDOUT of ChIPSeq pipeline ################################### ################################### STDOUT of ChIPSeq pipeline ###################################

== git info Latest git commit : f26ac9608ba2bdff10772b5cf24f0e3a259412b6 (Tue May 9 23:50:11 2017) Reading parameters from section (default) in file(tools/TF_chipseq_pipeline/default.env)...

== configuration file info Hostname : lm-4r10-n70.guillimin.clumeq.ca Configuration file : Environment file : tools/TF_chipseq_pipeline/default.env

Warning: Maximum # threads (-nth) for a pipeline is <= 1. Turning off parallelization... (-no_par)

== parallelization info No parallel jobs : true Maximum # threads : 1

== cluster/system info Walltime (general) : 5h50m Max. memory (general) : 7G Force to use a system : local Process priority (niceness) : 0 Retiral for failed tasks : 0 Submit tasks to a cluster queue : Unlimited cluster mem./walltime : false

== shell environment info Conda env. : aquas_chipseq Conda env. for python3 : aquas_chipseq_py3 Conda bin. directory :

Shell cmd. for init. : if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

Shell cmd. for init.(py3) : if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source activate aquas_chipseq_py3; sleep 5; fi; export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

Shell cmd. for fin. : TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

Cluster task min. len. : 60

Cluster task delay : 0

== output directory/title info Output dir. : ChIPSeq/160130_CTCF Title (prefix) : 160130_CTCF Reading parameters from section (default) in file(tools/TF_chipseq_pipeline/default.env)... Reading parameters from section (hg19) in file(tools/TF_chipseq_pipeline/Genomes/aquas_chipseq_species.conf)...

== species settings Species : hg19 Species file : tools/TF_chipseq_pipeline/Genomes/aquas_chipseq_species.conf

Species name (WashU browser) : hg19 Ref. genome seq. fasta : tools/TF_chipseq_pipeline/Genomes/hg19/male.hg19.fa Chr. sizes file : tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes Black list bed : tools/TF_chipseq_pipeline/Genomes/hg19/wgEncodeDacMapabilityConsensusExcludable.bed.gz Ref. genome seq. dir. :

== ENCODE accession settings ENCODE experiment accession : ENCODE award RFA : ENCODE assay category : ENCODE assay title : ENCODE award : ENCODE lab : ENCODE assembly genome : ENCODE alias prefix : KLAB_PIPELINE

== report settings URL root for output directory : Genome coord. for browser tracks :

== align bwa settings Param. for bwa : -q 5 -l 32 -k 2 BWA index : tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa Walltime (bwa) : 47h Max. memory (bwa) : 12G

== align multimapping settings

alignments reported for multimapping : 0

== postalign bam settings MAPQ reads rm thresh. : 30 Rm. tag reads with str. : No dupe removal in filtering raw bam : false Walltime (bam filter) : 23h Max. memory (bam filter) : 12G Dup marker : picard Use sambamba markdup (instead of picard) : false

== postalign bed/tagalign settings Max. memory for UNIX shuf : 12G

== postalign cross-corr. analysis settings Max. memory for UNIX shuf : 12G User-defined cross-corr. peak strandshift : -1 Extra parameters for cross-corr. analysis :

== callpeak spp settings Threshold for # peak : 300000 Walltime (spp) : 47h Max. memory (spp) : 12G Stack size for run_spp.R : Use-defined cross-corr. peak strandshift; if -1, use frag. len. :-1 Extra parameters for run_spp.R :

== callpeak gem settings Threshold for # peak in GEM : 300000 Min. length of k-mers in GEM : 6 Max. length of k-mers in GEM : 13 Q-value threshold for GEM : 0.0 Read distribution txt for GEM : tools/TF_chipseq_pipeline/etc/Read_Distribution_default.txt Extra parameters for GEM : Walltime (GEM) : 47h Max. memory (GEM) : 15G

== callpeak PeakSeq settings Target FDR for PeakSeq :0.05 Number of simulations for PeakSeq :10 Enrichment mapped frag. len. for PeakSeq :-1 Minimum interpeak distance for PeakSeq :-1 Mappability map file for PeakSeq : Maximum Q-value for PeakSeq :0.1 Background model for PeakSeq :Simulated Extra parameters for PeakSeq : Walltime (PeakSeq) : 47h Max. memory (PeakSeq) : 12G

== callpeak macs2 settings Genome size (hs,mm) : hs Walltime (macs2) : 23h Max. memory (macs2) : 15G P-value cutoff (macs2 callpeak) : 0.01 --keep-dup (macs2 callpeak) : all --extsize (macs2 callpeak); if -1 then use frag. len. : -1 --shift (macs2 callpeak) : 0 Extra parameters for macs2 callpeak :

== callpeak naiver overlap settings Bedtools intersect -nonamecheck : false

== IDR settings Append IDR threshold to IDR out_dir : false

== chipseq pipeline settings

replicates : 1

Type of ChIP-Seq pipeline : TF Final stage for ChIP-Seq : peak Signal tracks for pooled rep. only : false Aligner to map raw reads : bwa

reads to subsample for cross-corr. analysis : 15000000

reads to subsample exp. replicates (0: no subsampling): 0

reads to subsample controls (0: no subsampling) : 0

Generate anonymized filt. bam : false Peak caller for IDR analysis : spp Control rep. depth ratio : 1.2 Scoring column for IDR : signal.value IDR threshold : 0.05 Force to use pooled ctl : false Peak calling for true reps only : false No peak calling for self pseudo reps : false Disable cross-correlation analysis : false Disable g. peak filt. thru. n. peak : false

== checking chipseq parameters ...

== checking input files ...

Rep1 fastq (PE) : ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq Control Rep1 fastq (PE) : ChIPSeq/HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq ChIPSeq/HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq Distributing 1 to ... {rep1=1, ctl1=1} Distributing 1 to ... [1, 1] Task has finished (4516 seconds). bds -c tools/TF_chipseq_pipeline/bds.config -v tools/TF_chipseq_pipeline/chipseq.bds -title 160130_CTCF -final_stage peak -gensz hs -out_dir ChIPSeq/160130_CTCF -chrsz tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes -nth 1 -type TF -species hg19 -bwa_idx tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa -pe1 -fastq1_1:1 HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq -fastq1_2:1 HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq -ctl_pe1 -ctl_fastq1_1:1 HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq -ctl_fastq1_2:1 HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq

################################### chipseq.bds.20170602_104615_132.report.html ################################### ################################### chipseq.bds.20170602_104615_132.report.html ################################### ################################### chipseq.bds.20170602_104615_132.report.html ###################################

chipseq.bds.20170602_104615_132.report.html

BigDataScript report: chipseq.bds

Script file tools/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170602_104615_132
Start time 2017-06-02 10:46:15
Run time 01:17:42.170
Tasks executed 2
Tasks failed 1
Tasks failed names 
dedup_bam_PE_1 rep1
Arguments* [-title, 160130_CTCF, -final_stage, peak, -gensz, hs, -out_dir, ChIPSeq/160130_CTCF, -chrsz, tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes, -nth, 1, -type, TF, -species, hg19, -bwa_idx, tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa, -pe1, -fastq1_1:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq, -fastq1_2:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq, -ctl_pe1, -ctl_fastq1_1:1, HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq, -ctl_fastq1_2:1, HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq]
System* local
Cpus* -1
Exit value 1
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None 
 chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10
chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.align_bwa.bwa_sam_PE_rep1.line_181.id_10
Name bwa_sam_PE rep1
Thread thread_Root
PID 15573
OK true
Exit Code 0
Retries
State FINISHED
Dep. OK
Cpus 1
Mem
Start 2017-06-02 10:46:23
End 2017-06-02 12:01:50
Elapsed 01:15:26
Timeout 00:00:-1
Wall Timeout 100 days
Input files ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.sai
Output files ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam ChIPSeq/160130_CTCF/qc/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.flagstat.qc
Dependencies 
 
# SYS command. line 183

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 185

 bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.sai ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq | pigz -p 1 -nc > ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz

# SYS command. line 194

 pigz -p 1 -cd ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz \
            | awk 'BEGIN {FS="\t" ; OFS="\t"} ! /^@/ && $6!="*" { cigar=$6; gsub("[0-9]+D","",cigar); n = split(cigar,vals,"[A-Z]"); s = 0; for (i=1;i<=n;i++) s=s+vals[i]; seqlen=length($10) ; if (s!=seqlen) print $1"\t"; }' \
            | sort | uniq > ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads

# SYS command. line 199

 if [ $(cat ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads | wc -l) -gt 0 ]; then \
                zcat ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz | grep -v -F -f ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads | samtools view -Su - | samtools sort - ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE; \
            else \
                samtools view -Su ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz | samtools sort - ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE; \
            fi

# SYS command. line 211

 samtools flagstat ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam > ChIPSeq/160130_CTCF/qc/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.flagstat.qc

# SYS command. line 212

 samtools index ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam

# SYS command. line 216

 rm -f ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz

# SYS command. line 218

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
 
   
--------------------Stdout--------------------
Task has finished (4516 seconds).

--------------------Stderr--------------------
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 225438 pairs: 243.286 +/- 54.364
[infer_isize] skewness: 0.538; kurtosis: 0.215; ap_prior: 5.31e-05
[infer_isize] inferred maximum insert size: 621 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.77 sec
[bwa_sai2sam_pe_core] changing coordinates of 3673 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9767 out of 10967 Q17 singletons are mated.
[bwa_paired_sw] 294 out of 2210 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.18 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.01 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 241492 pairs: 242.723 +/- 54.198
[infer_isize] skewness: 0.537; kurtosis: 0.219; ap_prior: 5.16e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.51 sec
[bwa_sai2sam_pe_core] changing coordinates of 1098 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9024 out of 10229 Q17 singletons are mated.
[bwa_paired_sw] 41 out of 2130 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.07 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.82 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 240809 pairs: 241.415 +/- 54.160
[infer_isize] skewness: 0.560; kurtosis: 0.271; ap_prior: 7.05e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.61 sec
[bwa_sai2sam_pe_core] changing coordinates of 1463 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7369 out of 8510 Q17 singletons are mated.
[bwa_paired_sw] 89 out of 2716 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.98 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 279)
[infer_isize] low and high boundaries: 125 and 429 for estimating avg and std
[infer_isize] inferred external isize from 193449 pairs: 241.079 +/- 54.501
[infer_isize] skewness: 0.551; kurtosis: 0.227; ap_prior: 1.42e-04
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.97 sec
[bwa_sai2sam_pe_core] changing coordinates of 6994 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 25842 out of 27807 Q17 singletons are mated.
[bwa_paired_sw] 3030 out of 12986 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 3.99 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.00 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 279)
[infer_isize] low and high boundaries: 125 and 429 for estimating avg and std
[infer_isize] inferred external isize from 200644 pairs: 242.543 +/- 54.549
[infer_isize] skewness: 0.549; kurtosis: 0.240; ap_prior: 5.19e-05
[infer_isize] inferred maximum insert size: 621 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.78 sec
[bwa_sai2sam_pe_core] changing coordinates of 11570 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8913 out of 9939 Q17 singletons are mated.
[bwa_paired_sw] 567 out of 2654 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.19 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.02 sec
[bwa_sai2sam_pe_core] print alignments... 1.47 sec
[bwa_sai2sam_pe_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239159 pairs: 241.662 +/- 54.133
[infer_isize] skewness: 0.555; kurtosis: 0.271; ap_prior: 6.82e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.60 sec
[bwa_sai2sam_pe_core] changing coordinates of 1707 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7599 out of 8778 Q17 singletons are mated.
[bwa_paired_sw] 89 out of 2607 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.99 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.93 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 237, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 242340 pairs: 241.311 +/- 54.204
[infer_isize] skewness: 0.571; kurtosis: 0.276; ap_prior: 7.63e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.90 sec
[bwa_sai2sam_pe_core] changing coordinates of 1303 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6817 out of 7968 Q17 singletons are mated.
[bwa_paired_sw] 67 out of 2787 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.93 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 241325 pairs: 242.727 +/- 53.973
[infer_isize] skewness: 0.532; kurtosis: 0.239; ap_prior: 5.15e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.75 sec
[bwa_sai2sam_pe_core] changing coordinates of 1497 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7764 out of 8920 Q17 singletons are mated.
[bwa_paired_sw] 48 out of 2150 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.98 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.82 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 237866 pairs: 241.906 +/- 53.992
[infer_isize] skewness: 0.544; kurtosis: 0.246; ap_prior: 6.36e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.58 sec
[bwa_sai2sam_pe_core] changing coordinates of 1856 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7057 out of 8173 Q17 singletons are mated.
[bwa_paired_sw] 81 out of 2503 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.95 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.86 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 236883 pairs: 241.639 +/- 54.175
[infer_isize] skewness: 0.556; kurtosis: 0.249; ap_prior: 6.79e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.89 sec
[bwa_sai2sam_pe_core] changing coordinates of 2192 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8494 out of 9686 Q17 singletons are mated.
[bwa_paired_sw] 149 out of 2672 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.07 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.01 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 239923 pairs: 242.138 +/- 54.082
[infer_isize] skewness: 0.543; kurtosis: 0.228; ap_prior: 6.51e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.19 sec
[bwa_sai2sam_pe_core] changing coordinates of 865 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9328 out of 11155 Q17 singletons are mated.
[bwa_paired_sw] 61 out of 2558 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241349 pairs: 241.734 +/- 54.166
[infer_isize] skewness: 0.555; kurtosis: 0.263; ap_prior: 6.91e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.43 sec
[bwa_sai2sam_pe_core] changing coordinates of 1241 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8196 out of 9436 Q17 singletons are mated.
[bwa_paired_sw] 48 out of 2547 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.03 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 172352 pairs: 241.563 +/- 54.324
[infer_isize] skewness: 0.550; kurtosis: 0.239; ap_prior: 7.33e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.92 sec
[bwa_sai2sam_pe_core] changing coordinates of 10130 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7724 out of 8696 Q17 singletons are mated.
[bwa_paired_sw] 948 out of 3502 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.24 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.06 sec
[bwa_sai2sam_pe_core] print alignments... 1.32 sec
[bwa_sai2sam_pe_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 222023 pairs: 241.686 +/- 54.293
[infer_isize] skewness: 0.553; kurtosis: 0.245; ap_prior: 7.01e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.25 sec
[bwa_sai2sam_pe_core] changing coordinates of 5699 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7165 out of 8362 Q17 singletons are mated.
[bwa_paired_sw] 216 out of 2754 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.98 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec
[bwa_sai2sam_pe_core] print alignments... 1.42 sec
[bwa_sai2sam_pe_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 237, 277)
[infer_isize] low and high boundaries: 125 and 423 for estimating avg and std
[infer_isize] inferred external isize from 240218 pairs: 241.140 +/- 53.914
[infer_isize] skewness: 0.554; kurtosis: 0.242; ap_prior: 7.17e-05
[infer_isize] inferred maximum insert size: 615 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.64 sec
[bwa_sai2sam_pe_core] changing coordinates of 1472 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7182 out of 8405 Q17 singletons are mated.
[bwa_paired_sw] 99 out of 2734 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.95 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241089 pairs: 241.318 +/- 54.044
[infer_isize] skewness: 0.565; kurtosis: 0.273; ap_prior: 7.18e-05
[infer_isize] inferred maximum insert size: 616 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.18 sec
[bwa_sai2sam_pe_core] changing coordinates of 1451 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7645 out of 8811 Q17 singletons are mated.
[bwa_paired_sw] 100 out of 2706 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.98 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 237981 pairs: 242.180 +/- 54.232
[infer_isize] skewness: 0.549; kurtosis: 0.232; ap_prior: 6.82e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.26 sec
[bwa_sai2sam_pe_core] changing coordinates of 2050 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8988 out of 10230 Q17 singletons are mated.
[bwa_paired_sw] 158 out of 2672 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.10 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241952 pairs: 241.881 +/- 54.067
[infer_isize] skewness: 0.551; kurtosis: 0.257; ap_prior: 6.72e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.86 sec
[bwa_sai2sam_pe_core] changing coordinates of 1268 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7525 out of 8753 Q17 singletons are mated.
[bwa_paired_sw] 77 out of 2647 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.99 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.85 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 240858 pairs: 242.001 +/- 53.908
[infer_isize] skewness: 0.543; kurtosis: 0.239; ap_prior: 6.25e-05
[infer_isize] inferred maximum insert size: 616 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.24 sec
[bwa_sai2sam_pe_core] changing coordinates of 1080 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8431 out of 9750 Q17 singletons are mated.
[bwa_paired_sw] 114 out of 2579 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.06 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (203, 237, 277)
[infer_isize] low and high boundaries: 125 and 425 for estimating avg and std
[infer_isize] inferred external isize from 240327 pairs: 241.033 +/- 54.127
[infer_isize] skewness: 0.565; kurtosis: 0.269; ap_prior: 7.44e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.75 sec
[bwa_sai2sam_pe_core] changing coordinates of 1705 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6876 out of 8054 Q17 singletons are mated.
[bwa_paired_sw] 89 out of 2797 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.93 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 240821 pairs: 241.744 +/- 54.086
[infer_isize] skewness: 0.546; kurtosis: 0.236; ap_prior: 6.68e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.04 sec
[bwa_sai2sam_pe_core] changing coordinates of 1832 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7051 out of 8278 Q17 singletons are mated.
[bwa_paired_sw] 128 out of 2687 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.96 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.85 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 238571 pairs: 241.322 +/- 54.103
[infer_isize] skewness: 0.561; kurtosis: 0.262; ap_prior: 6.96e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.82 sec
[bwa_sai2sam_pe_core] changing coordinates of 1915 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8050 out of 9325 Q17 singletons are mated.
[bwa_paired_sw] 156 out of 2792 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.03 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.93 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 233693 pairs: 242.018 +/- 54.014
[infer_isize] skewness: 0.544; kurtosis: 0.226; ap_prior: 6.09e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.32 sec
[bwa_sai2sam_pe_core] changing coordinates of 2837 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7822 out of 9072 Q17 singletons are mated.
[bwa_paired_sw] 202 out of 2541 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.03 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 193233 pairs: 241.293 +/- 54.170
[infer_isize] skewness: 0.569; kurtosis: 0.260; ap_prior: 8.38e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.76 sec
[bwa_sai2sam_pe_core] changing coordinates of 1940 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7543 out of 8634 Q17 singletons are mated.
[bwa_paired_sw] 263 out of 2722 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.05 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.83 sec
[bwa_sai2sam_pe_core] print alignments... 1.21 sec
[bwa_sai2sam_pe_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 236541 pairs: 241.292 +/- 54.154
[infer_isize] skewness: 0.568; kurtosis: 0.269; ap_prior: 7.80e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.72 sec
[bwa_sai2sam_pe_core] changing coordinates of 2010 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8347 out of 9632 Q17 singletons are mated.
[bwa_paired_sw] 124 out of 3002 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.07 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.99 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (203, 237, 277)
[infer_isize] low and high boundaries: 125 and 425 for estimating avg and std
[infer_isize] inferred external isize from 239347 pairs: 240.791 +/- 54.158
[infer_isize] skewness: 0.576; kurtosis: 0.286; ap_prior: 7.98e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.77 sec
[bwa_sai2sam_pe_core] changing coordinates of 2427 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6503 out of 7723 Q17 singletons are mated.
[bwa_paired_sw] 116 out of 2984 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.92 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 237, 277)
[infer_isize] low and high boundaries: 125 and 423 for estimating avg and std
[infer_isize] inferred external isize from 240281 pairs: 240.937 +/- 53.952
[infer_isize] skewness: 0.552; kurtosis: 0.235; ap_prior: 7.56e-05
[infer_isize] inferred maximum insert size: 615 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.27 sec
[bwa_sai2sam_pe_core] changing coordinates of 2012 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6640 out of 7894 Q17 singletons are mated.
[bwa_paired_sw] 108 out of 2899 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.94 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239755 pairs: 241.239 +/- 54.064
[infer_isize] skewness: 0.559; kurtosis: 0.265; ap_prior: 7.83e-05
[infer_isize] inferred maximum insert size: 616 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.05 sec
[bwa_sai2sam_pe_core] changing coordinates of 1549 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8247 out of 9546 Q17 singletons are mated.
[bwa_paired_sw] 116 out of 2969 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.05 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.10 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 233124 pairs: 241.583 +/- 54.418
[infer_isize] skewness: 0.568; kurtosis: 0.257; ap_prior: 8.01e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.85 sec
[bwa_sai2sam_pe_core] changing coordinates of 3221 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7800 out of 9095 Q17 singletons are mated.
[bwa_paired_sw] 251 out of 3123 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 237, 277)
[infer_isize] low and high boundaries: 125 and 423 for estimating avg and std
[infer_isize] inferred external isize from 234349 pairs: 240.959 +/- 53.752
[infer_isize] skewness: 0.559; kurtosis: 0.261; ap_prior: 7.72e-05
[infer_isize] inferred maximum insert size: 614 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.25 sec
[bwa_sai2sam_pe_core] changing coordinates of 3343 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7231 out of 8437 Q17 singletons are mated.
[bwa_paired_sw] 178 out of 2970 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 224990 pairs: 241.336 +/- 54.117
[infer_isize] skewness: 0.559; kurtosis: 0.265; ap_prior: 6.96e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.75 sec
[bwa_sai2sam_pe_core] changing coordinates of 3464 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6777 out of 7945 Q17 singletons are mated.
[bwa_paired_sw] 106 out of 2651 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.93 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (203, 237, 277)
[infer_isize] low and high boundaries: 125 and 425 for estimating avg and std
[infer_isize] inferred external isize from 239668 pairs: 240.865 +/- 54.172
[infer_isize] skewness: 0.570; kurtosis: 0.266; ap_prior: 8.10e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.54 sec
[bwa_sai2sam_pe_core] changing coordinates of 2219 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7007 out of 8265 Q17 singletons are mated.
[bwa_paired_sw] 105 out of 3048 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.97 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.86 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 237, 277)
[infer_isize] low and high boundaries: 125 and 423 for estimating avg and std
[infer_isize] inferred external isize from 240999 pairs: 240.997 +/- 54.002
[infer_isize] skewness: 0.548; kurtosis: 0.227; ap_prior: 7.84e-05
[infer_isize] inferred maximum insert size: 616 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.18 sec
[bwa_sai2sam_pe_core] changing coordinates of 1584 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6983 out of 8260 Q17 singletons are mated.
[bwa_paired_sw] 105 out of 3003 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.95 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.86 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 241818 pairs: 242.106 +/- 53.944
[infer_isize] skewness: 0.538; kurtosis: 0.229; ap_prior: 5.80e-05
[infer_isize] inferred maximum insert size: 616 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.59 sec
[bwa_sai2sam_pe_core] changing coordinates of 982 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8846 out of 10204 Q17 singletons are mated.
[bwa_paired_sw] 169 out of 2541 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.04 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 242516 pairs: 241.863 +/- 54.087
[infer_isize] skewness: 0.550; kurtosis: 0.243; ap_prior: 6.43e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.97 sec
[bwa_sai2sam_pe_core] changing coordinates of 1028 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7618 out of 8924 Q17 singletons are mated.
[bwa_paired_sw] 65 out of 2562 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.97 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 230394 pairs: 242.300 +/- 54.089
[infer_isize] skewness: 0.530; kurtosis: 0.193; ap_prior: 5.54e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.21 sec
[bwa_sai2sam_pe_core] changing coordinates of 2970 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9675 out of 10954 Q17 singletons are mated.
[bwa_paired_sw] 116 out of 2348 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.13 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.02 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239699 pairs: 241.969 +/- 54.184
[infer_isize] skewness: 0.565; kurtosis: 0.277; ap_prior: 6.32e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.66 sec
[bwa_sai2sam_pe_core] changing coordinates of 1142 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9145 out of 10510 Q17 singletons are mated.
[bwa_paired_sw] 83 out of 2524 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 241996 pairs: 242.065 +/- 53.988
[infer_isize] skewness: 0.539; kurtosis: 0.234; ap_prior: 6.31e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.72 sec
[bwa_sai2sam_pe_core] changing coordinates of 952 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8374 out of 9615 Q17 singletons are mated.
[bwa_paired_sw] 80 out of 2557 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.05 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (203, 237, 278)
[infer_isize] low and high boundaries: 125 and 428 for estimating avg and std
[infer_isize] inferred external isize from 234205 pairs: 240.975 +/- 54.236
[infer_isize] skewness: 0.581; kurtosis: 0.304; ap_prior: 1.08e-04
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.49 sec
[bwa_sai2sam_pe_core] changing coordinates of 4314 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7508 out of 8772 Q17 singletons are mated.
[bwa_paired_sw] 164 out of 3204 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.06 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241409 pairs: 241.337 +/- 54.067
[infer_isize] skewness: 0.575; kurtosis: 0.292; ap_prior: 7.61e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.07 sec
[bwa_sai2sam_pe_core] changing coordinates of 1593 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6648 out of 7949 Q17 singletons are mated.
[bwa_paired_sw] 86 out of 2921 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.92 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 242318 pairs: 241.163 +/- 54.208
[infer_isize] skewness: 0.565; kurtosis: 0.265; ap_prior: 7.16e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.26 sec
[bwa_sai2sam_pe_core] changing coordinates of 1123 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7132 out of 8387 Q17 singletons are mated.
[bwa_paired_sw] 61 out of 2758 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.95 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.85 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 279)
[infer_isize] low and high boundaries: 125 and 429 for estimating avg and std
[infer_isize] inferred external isize from 232642 pairs: 242.107 +/- 54.538
[infer_isize] skewness: 0.559; kurtosis: 0.272; ap_prior: 8.50e-05
[infer_isize] inferred maximum insert size: 621 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.37 sec
[bwa_sai2sam_pe_core] changing coordinates of 2939 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8947 out of 10345 Q17 singletons are mated.
[bwa_paired_sw] 470 out of 2878 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.18 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 237944 pairs: 241.449 +/- 54.241
[infer_isize] skewness: 0.566; kurtosis: 0.256; ap_prior: 6.93e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.24 sec
[bwa_sai2sam_pe_core] changing coordinates of 1803 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9422 out of 10715 Q17 singletons are mated.
[bwa_paired_sw] 90 out of 2655 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.11 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241589 pairs: 241.877 +/- 54.100
[infer_isize] skewness: 0.554; kurtosis: 0.261; ap_prior: 6.48e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.86 sec
[bwa_sai2sam_pe_core] changing coordinates of 1718 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7173 out of 8446 Q17 singletons are mated.
[bwa_paired_sw] 97 out of 2664 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.98 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 280)
[infer_isize] low and high boundaries: 125 and 432 for estimating avg and std
[infer_isize] inferred external isize from 209044 pairs: 241.522 +/- 54.806
[infer_isize] skewness: 0.589; kurtosis: 0.332; ap_prior: 2.16e-04
[infer_isize] inferred maximum insert size: 622 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.25 sec
[bwa_sai2sam_pe_core] changing coordinates of 9141 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7974 out of 9114 Q17 singletons are mated.
[bwa_paired_sw] 2363 out of 5908 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.68 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.99 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 237, 277)
[infer_isize] low and high boundaries: 125 and 423 for estimating avg and std
[infer_isize] inferred external isize from 221239 pairs: 241.071 +/- 53.998
[infer_isize] skewness: 0.549; kurtosis: 0.224; ap_prior: 6.78e-05
[infer_isize] inferred maximum insert size: 616 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.12 sec
[bwa_sai2sam_pe_core] changing coordinates of 5527 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9036 out of 10330 Q17 singletons are mated.
[bwa_paired_sw] 137 out of 2666 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.98 sec
[bwa_sai2sam_pe_core] print alignments... 1.42 sec
[bwa_sai2sam_pe_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 218609 pairs: 241.787 +/- 54.166
[infer_isize] skewness: 0.555; kurtosis: 0.252; ap_prior: 7.90e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.84 sec
[bwa_sai2sam_pe_core] changing coordinates of 4611 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 10112 out of 11387 Q17 singletons are mated.
[bwa_paired_sw] 126 out of 2491 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.18 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.05 sec
[bwa_sai2sam_pe_core] print alignments... 1.42 sec
[bwa_sai2sam_pe_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 237, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 242319 pairs: 241.220 +/- 54.138
[infer_isize] skewness: 0.564; kurtosis: 0.266; ap_prior: 7.51e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.75 sec
[bwa_sai2sam_pe_core] changing coordinates of 1436 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6544 out of 7804 Q17 singletons are mated.
[bwa_paired_sw] 86 out of 2933 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.91 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 232523 pairs: 241.792 +/- 54.116
[infer_isize] skewness: 0.550; kurtosis: 0.239; ap_prior: 6.30e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.38 sec
[bwa_sai2sam_pe_core] changing coordinates of 2633 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9185 out of 10503 Q17 singletons are mated.
[bwa_paired_sw] 129 out of 2574 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.10 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 232904 pairs: 242.020 +/- 54.229
[infer_isize] skewness: 0.549; kurtosis: 0.242; ap_prior: 6.33e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.51 sec
[bwa_sai2sam_pe_core] changing coordinates of 3660 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9223 out of 10590 Q17 singletons are mated.
[bwa_paired_sw] 188 out of 2627 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.15 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.01 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 219802 pairs: 241.772 +/- 54.243
[infer_isize] skewness: 0.566; kurtosis: 0.258; ap_prior: 7.47e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 10.74 sec
[bwa_sai2sam_pe_core] changing coordinates of 3894 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7542 out of 8921 Q17 singletons are mated.
[bwa_paired_sw] 172 out of 2869 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.81 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 217339 pairs: 241.578 +/- 54.285
[infer_isize] skewness: 0.561; kurtosis: 0.269; ap_prior: 7.24e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 9.32 sec
[bwa_sai2sam_pe_core] changing coordinates of 5582 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7345 out of 8649 Q17 singletons are mated.
[bwa_paired_sw] 402 out of 3103 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.04 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.97 sec
[bwa_sai2sam_pe_core] print alignments... 1.44 sec
[bwa_sai2sam_pe_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 207599 pairs: 241.946 +/- 54.334
[infer_isize] skewness: 0.557; kurtosis: 0.251; ap_prior: 6.88e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.03 sec
[bwa_sai2sam_pe_core] changing coordinates of 2486 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7069 out of 8259 Q17 singletons are mated.
[bwa_paired_sw] 123 out of 2524 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.96 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.29 sec
[bwa_sai2sam_pe_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 237102 pairs: 241.269 +/- 54.105
[infer_isize] skewness: 0.558; kurtosis: 0.271; ap_prior: 7.43e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.94 sec
[bwa_sai2sam_pe_core] changing coordinates of 1746 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7152 out of 8466 Q17 singletons are mated.
[bwa_paired_sw] 95 out of 2884 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.95 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.86 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241742 pairs: 241.442 +/- 54.195
[infer_isize] skewness: 0.565; kurtosis: 0.269; ap_prior: 7.46e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.97 sec
[bwa_sai2sam_pe_core] changing coordinates of 1357 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6962 out of 8292 Q17 singletons are mated.
[bwa_paired_sw] 91 out of 2910 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.96 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.93 sec
[bwa_sai2sam_pe_core] print alignments... 1.42 sec
[bwa_sai2sam_pe_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 237545 pairs: 242.005 +/- 54.241
[infer_isize] skewness: 0.546; kurtosis: 0.234; ap_prior: 6.70e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.27 sec
[bwa_sai2sam_pe_core] changing coordinates of 1859 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7586 out of 8886 Q17 singletons are mated.
[bwa_paired_sw] 176 out of 2795 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.01 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 165910 pairs: 241.445 +/- 54.164
[infer_isize] skewness: 0.556; kurtosis: 0.255; ap_prior: 6.87e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.99 sec
[bwa_sai2sam_pe_core] changing coordinates of 10492 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6833 out of 7929 Q17 singletons are mated.
[bwa_paired_sw] 575 out of 2957 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.06 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.05 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239475 pairs: 241.925 +/- 54.169
[infer_isize] skewness: 0.550; kurtosis: 0.242; ap_prior: 6.71e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.42 sec
[bwa_sai2sam_pe_core] changing coordinates of 1769 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7245 out of 8509 Q17 singletons are mated.
[bwa_paired_sw] 57 out of 2667 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.96 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.83 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 236985 pairs: 242.755 +/- 54.228
[infer_isize] skewness: 0.538; kurtosis: 0.221; ap_prior: 5.33e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.23 sec
[bwa_sai2sam_pe_core] changing coordinates of 1542 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9598 out of 10961 Q17 singletons are mated.
[bwa_paired_sw] 205 out of 2501 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.17 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 240, 283)
[infer_isize] low and high boundaries: 125 and 439 for estimating avg and std
[infer_isize] inferred external isize from 164815 pairs: 241.293 +/- 54.960
[infer_isize] skewness: 0.609; kurtosis: 0.423; ap_prior: 4.07e-04
[infer_isize] inferred maximum insert size: 623 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.31 sec
[bwa_sai2sam_pe_core] changing coordinates of 11751 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 16477 out of 17913 Q17 singletons are mated.
[bwa_paired_sw] 6646 out of 14896 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 3.94 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.29 sec
[bwa_sai2sam_pe_core] print alignments... 1.31 sec
[bwa_sai2sam_pe_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 279)
[infer_isize] low and high boundaries: 125 and 429 for estimating avg and std
[infer_isize] inferred external isize from 180808 pairs: 241.650 +/- 54.397
[infer_isize] skewness: 0.570; kurtosis: 0.289; ap_prior: 1.18e-04
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.54 sec
[bwa_sai2sam_pe_core] changing coordinates of 8446 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 18848 out of 20965 Q17 singletons are mated.
[bwa_paired_sw] 2413 out of 7478 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 2.75 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.03 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 237342 pairs: 242.157 +/- 53.980
[infer_isize] skewness: 0.544; kurtosis: 0.236; ap_prior: 5.96e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.93 sec
[bwa_sai2sam_pe_core] changing coordinates of 2125 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8926 out of 10371 Q17 singletons are mated.
[bwa_paired_sw] 83 out of 2468 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.07 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 236010 pairs: 242.648 +/- 54.404
[infer_isize] skewness: 0.550; kurtosis: 0.248; ap_prior: 6.07e-05
[infer_isize] inferred maximum insert size: 620 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.92 sec
[bwa_sai2sam_pe_core] changing coordinates of 1412 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8689 out of 10138 Q17 singletons are mated.
[bwa_paired_sw] 146 out of 2542 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.09 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239670 pairs: 241.812 +/- 54.151
[infer_isize] skewness: 0.553; kurtosis: 0.237; ap_prior: 7.06e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.94 sec
[bwa_sai2sam_pe_core] changing coordinates of 1772 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7567 out of 8903 Q17 singletons are mated.
[bwa_paired_sw] 119 out of 2821 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 222796 pairs: 242.972 +/- 54.182
[infer_isize] skewness: 0.540; kurtosis: 0.222; ap_prior: 5.34e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.45 sec
[bwa_sai2sam_pe_core] changing coordinates of 1866 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9087 out of 10416 Q17 singletons are mated.
[bwa_paired_sw] 179 out of 2372 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.11 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec
[bwa_sai2sam_pe_core] print alignments... 1.35 sec
[bwa_sai2sam_pe_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 238431 pairs: 241.573 +/- 54.091
[infer_isize] skewness: 0.561; kurtosis: 0.274; ap_prior: 6.92e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.26 sec
[bwa_sai2sam_pe_core] changing coordinates of 2225 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7661 out of 9041 Q17 singletons are mated.
[bwa_paired_sw] 100 out of 2855 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 238517 pairs: 242.691 +/- 54.200
[infer_isize] skewness: 0.534; kurtosis: 0.215; ap_prior: 5.24e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.15 sec
[bwa_sai2sam_pe_core] changing coordinates of 1554 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9296 out of 10655 Q17 singletons are mated.
[bwa_paired_sw] 75 out of 2253 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.09 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239624 pairs: 241.711 +/- 54.205
[infer_isize] skewness: 0.566; kurtosis: 0.267; ap_prior: 7.25e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.91 sec
[bwa_sai2sam_pe_core] changing coordinates of 1734 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8306 out of 9642 Q17 singletons are mated.
[bwa_paired_sw] 199 out of 2983 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.06 sec
[bwa_sai2sam_pe_core] print alignments... 1.42 sec
[bwa_sai2sam_pe_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 236157 pairs: 242.325 +/- 54.285
[infer_isize] skewness: 0.543; kurtosis: 0.234; ap_prior: 5.99e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.91 sec
[bwa_sai2sam_pe_core] changing coordinates of 1344 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9037 out of 10480 Q17 singletons are mated.
[bwa_paired_sw] 170 out of 2642 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.11 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec
[bwa_sai2sam_pe_core] print alignments... 1.37 sec
[bwa_sai2sam_pe_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 238149 pairs: 241.347 +/- 54.168
[infer_isize] skewness: 0.565; kurtosis: 0.271; ap_prior: 6.74e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.20 sec
[bwa_sai2sam_pe_core] changing coordinates of 1932 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8677 out of 10299 Q17 singletons are mated.
[bwa_paired_sw] 164 out of 2811 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.05 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.93 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241676 pairs: 241.561 +/- 54.104
[infer_isize] skewness: 0.559; kurtosis: 0.266; ap_prior: 6.62e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.32 sec
[bwa_sai2sam_pe_core] changing coordinates of 1170 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7904 out of 9180 Q17 singletons are mated.
[bwa_paired_sw] 65 out of 2708 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 237795 pairs: 242.306 +/- 54.049
[infer_isize] skewness: 0.536; kurtosis: 0.207; ap_prior: 6.24e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.11 sec
[bwa_sai2sam_pe_core] changing coordinates of 1420 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 10665 out of 12145 Q17 singletons are mated.
[bwa_paired_sw] 138 out of 2651 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.21 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 240122 pairs: 241.747 +/- 54.155
[infer_isize] skewness: 0.560; kurtosis: 0.270; ap_prior: 6.81e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.03 sec
[bwa_sai2sam_pe_core] changing coordinates of 1405 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8267 out of 9643 Q17 singletons are mated.
[bwa_paired_sw] 100 out of 2824 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.04 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.01 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 237, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 238939 pairs: 241.117 +/- 54.132
[infer_isize] skewness: 0.572; kurtosis: 0.292; ap_prior: 7.93e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.52 sec
[bwa_sai2sam_pe_core] changing coordinates of 1734 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7713 out of 9032 Q17 singletons are mated.
[bwa_paired_sw] 112 out of 3134 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.01 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 237, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241223 pairs: 241.199 +/- 54.272
[infer_isize] skewness: 0.576; kurtosis: 0.288; ap_prior: 8.00e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.70 sec
[bwa_sai2sam_pe_core] changing coordinates of 1145 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7723 out of 9021 Q17 singletons are mated.
[bwa_paired_sw] 75 out of 3055 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.01 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.00 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 228855 pairs: 241.991 +/- 54.371
[infer_isize] skewness: 0.560; kurtosis: 0.262; ap_prior: 7.11e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.40 sec
[bwa_sai2sam_pe_core] changing coordinates of 3584 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8220 out of 9625 Q17 singletons are mated.
[bwa_paired_sw] 203 out of 2908 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.07 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.06 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239673 pairs: 241.343 +/- 54.120
[infer_isize] skewness: 0.559; kurtosis: 0.268; ap_prior: 7.46e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.23 sec
[bwa_sai2sam_pe_core] changing coordinates of 1652 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7887 out of 9252 Q17 singletons are mated.
[bwa_paired_sw] 95 out of 3074 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.03 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 241111 pairs: 241.994 +/- 53.964
[infer_isize] skewness: 0.550; kurtosis: 0.235; ap_prior: 6.18e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.63 sec
[bwa_sai2sam_pe_core] changing coordinates of 811 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8984 out of 10444 Q17 singletons are mated.
[bwa_paired_sw] 70 out of 2524 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.06 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 241787 pairs: 242.718 +/- 54.491
[infer_isize] skewness: 0.548; kurtosis: 0.238; ap_prior: 5.57e-05
[infer_isize] inferred maximum insert size: 621 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.12 sec
[bwa_sai2sam_pe_core] changing coordinates of 560 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9140 out of 10732 Q17 singletons are mated.
[bwa_paired_sw] 39 out of 2368 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 211208 pairs: 241.952 +/- 54.254
[infer_isize] skewness: 0.550; kurtosis: 0.245; ap_prior: 7.35e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.26 sec
[bwa_sai2sam_pe_core] changing coordinates of 6941 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9654 out of 11048 Q17 singletons are mated.
[bwa_paired_sw] 713 out of 3672 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.34 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.02 sec
[bwa_sai2sam_pe_core] print alignments... 1.44 sec
[bwa_sai2sam_pe_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 232720 pairs: 242.181 +/- 54.097
[infer_isize] skewness: 0.537; kurtosis: 0.208; ap_prior: 5.86e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.92 sec
[bwa_sai2sam_pe_core] changing coordinates of 2321 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8616 out of 10046 Q17 singletons are mated.
[bwa_paired_sw] 227 out of 2662 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 230618 pairs: 242.563 +/- 54.232
[infer_isize] skewness: 0.542; kurtosis: 0.236; ap_prior: 5.70e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.50 sec
[bwa_sai2sam_pe_core] changing coordinates of 3391 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9369 out of 10877 Q17 singletons are mated.
[bwa_paired_sw] 164 out of 2452 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.13 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 239, 280)
[infer_isize] low and high boundaries: 125 and 432 for estimating avg and std
[infer_isize] inferred external isize from 175886 pairs: 242.093 +/- 54.809
[infer_isize] skewness: 0.575; kurtosis: 0.310; ap_prior: 1.50e-04
[infer_isize] inferred maximum insert size: 622 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.88 sec
[bwa_sai2sam_pe_core] changing coordinates of 14849 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 10410 out of 11647 Q17 singletons are mated.
[bwa_paired_sw] 1098 out of 3950 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.53 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.98 sec
[bwa_sai2sam_pe_core] print alignments... 1.45 sec
[bwa_sai2sam_pe_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 240042 pairs: 242.133 +/- 53.974
[infer_isize] skewness: 0.538; kurtosis: 0.219; ap_prior: 6.07e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.88 sec
[bwa_sai2sam_pe_core] changing coordinates of 1189 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8823 out of 10263 Q17 singletons are mated.
[bwa_paired_sw] 59 out of 2533 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.06 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 235826 pairs: 243.120 +/- 54.317
[infer_isize] skewness: 0.533; kurtosis: 0.212; ap_prior: 4.75e-05
[infer_isize] inferred maximum insert size: 620 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.85 sec
[bwa_sai2sam_pe_core] changing coordinates of 1184 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 11886 out of 13477 Q17 singletons are mated.
[bwa_paired_sw] 144 out of 2219 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.29 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.00 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 239, 279)
[infer_isize] low and high boundaries: 125 and 429 for estimating avg and std
[infer_isize] inferred external isize from 203989 pairs: 242.361 +/- 54.435
[infer_isize] skewness: 0.557; kurtosis: 0.255; ap_prior: 6.65e-05
[infer_isize] inferred maximum insert size: 620 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.81 sec
[bwa_sai2sam_pe_core] changing coordinates of 5352 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 11501 out of 13005 Q17 singletons are mated.
[bwa_paired_sw] 500 out of 3014 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.39 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 234558 pairs: 242.925 +/- 54.183
[infer_isize] skewness: 0.536; kurtosis: 0.228; ap_prior: 4.77e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.40 sec
[bwa_sai2sam_pe_core] changing coordinates of 2309 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 10097 out of 11556 Q17 singletons are mated.
[bwa_paired_sw] 77 out of 2200 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.14 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 238233 pairs: 242.014 +/- 54.015
[infer_isize] skewness: 0.546; kurtosis: 0.231; ap_prior: 6.17e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.16 sec
[bwa_sai2sam_pe_core] changing coordinates of 1779 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9106 out of 10609 Q17 singletons are mated.
[bwa_paired_sw] 112 out of 2578 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.09 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 232179 pairs: 243.228 +/- 54.536
[infer_isize] skewness: 0.531; kurtosis: 0.197; ap_prior: 4.67e-05
[infer_isize] inferred maximum insert size: 622 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.63 sec
[bwa_sai2sam_pe_core] changing coordinates of 1424 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 12265 out of 13789 Q17 singletons are mated.
[bwa_paired_sw] 233 out of 2436 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.42 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 221149 pairs: 241.475 +/- 54.270
[infer_isize] skewness: 0.571; kurtosis: 0.276; ap_prior: 7.39e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.19 sec
[bwa_sai2sam_pe_core] changing coordinates of 2589 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9311 out of 10672 Q17 singletons are mated.
[bwa_paired_sw] 223 out of 2908 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.14 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.89 sec
[bwa_sai2sam_pe_core] print alignments... 1.35 sec
[bwa_sai2sam_pe_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241875 pairs: 241.740 +/- 54.114
[infer_isize] skewness: 0.550; kurtosis: 0.239; ap_prior: 6.90e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.21 sec
[bwa_sai2sam_pe_core] changing coordinates of 1003 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7307 out of 8701 Q17 singletons are mated.
[bwa_paired_sw] 65 out of 2842 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.96 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.89 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 240216 pairs: 241.660 +/- 54.105
[infer_isize] skewness: 0.560; kurtosis: 0.269; ap_prior: 7.01e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.22 sec
[bwa_sai2sam_pe_core] changing coordinates of 979 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8792 out of 10260 Q17 singletons are mated.
[bwa_paired_sw] 121 out of 2866 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.09 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 234765 pairs: 242.776 +/- 54.312
[infer_isize] skewness: 0.551; kurtosis: 0.245; ap_prior: 5.67e-05
[infer_isize] inferred maximum insert size: 620 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.45 sec
[bwa_sai2sam_pe_core] changing coordinates of 1428 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8458 out of 9917 Q17 singletons are mated.
[bwa_paired_sw] 229 out of 2699 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.09 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.85 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 194632 pairs: 242.906 +/- 54.133
[infer_isize] skewness: 0.542; kurtosis: 0.248; ap_prior: 5.47e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.82 sec
[bwa_sai2sam_pe_core] changing coordinates of 1837 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 11734 out of 13338 Q17 singletons are mated.
[bwa_paired_sw] 319 out of 2430 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.34 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec
[bwa_sai2sam_pe_core] print alignments... 1.25 sec
[bwa_sai2sam_pe_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (206, 239, 279)
[infer_isize] low and high boundaries: 125 and 425 for estimating avg and std
[infer_isize] inferred external isize from 235487 pairs: 243.090 +/- 54.007
[infer_isize] skewness: 0.518; kurtosis: 0.189; ap_prior: 4.67e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.25 sec
[bwa_sai2sam_pe_core] changing coordinates of 688 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 14407 out of 16066 Q17 singletons are mated.
[bwa_paired_sw] 38 out of 2101 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.42 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 209885 pairs: 242.759 +/- 54.445
[infer_isize] skewness: 0.542; kurtosis: 0.225; ap_prior: 7.64e-05
[infer_isize] inferred maximum insert size: 621 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.09 sec
[bwa_sai2sam_pe_core] changing coordinates of 2187 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 18103 out of 20206 Q17 singletons are mated.
[bwa_paired_sw] 1580 out of 8401 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 2.68 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.97 sec
[bwa_sai2sam_pe_core] print alignments... 1.37 sec
[bwa_sai2sam_pe_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 214545 pairs: 242.922 +/- 54.190
[infer_isize] skewness: 0.531; kurtosis: 0.219; ap_prior: 5.74e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.82 sec
[bwa_sai2sam_pe_core] changing coordinates of 7312 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 12477 out of 14025 Q17 singletons are mated.
[bwa_paired_sw] 202 out of 2278 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.33 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.98 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 224301 pairs: 242.907 +/- 54.135
[infer_isize] skewness: 0.531; kurtosis: 0.218; ap_prior: 6.02e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.06 sec
[bwa_sai2sam_pe_core] changing coordinates of 4498 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8901 out of 10339 Q17 singletons are mated.
[bwa_paired_sw] 313 out of 2657 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.13 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 217409 pairs: 241.736 +/- 54.137
[infer_isize] skewness: 0.557; kurtosis: 0.261; ap_prior: 6.86e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.65 sec
[bwa_sai2sam_pe_core] changing coordinates of 3923 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 11035 out of 12609 Q17 singletons are mated.
[bwa_paired_sw] 474 out of 3372 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.38 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.16 sec
[bwa_sai2sam_pe_core] print alignments... 1.36 sec
[bwa_sai2sam_pe_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 131869 pairs: 242.488 +/- 54.584
[infer_isize] skewness: 0.540; kurtosis: 0.220; ap_prior: 7.70e-05
[infer_isize] inferred maximum insert size: 621 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.40 sec
[bwa_sai2sam_pe_core] changing coordinates of 5325 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 14489 out of 15932 Q17 singletons are mated.
[bwa_paired_sw] 1142 out of 3588 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.88 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.05 sec
[bwa_sai2sam_pe_core] print alignments... 1.08 sec
[bwa_sai2sam_pe_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (199, 234, 275)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 15370 pairs: 237.628 +/- 54.847
[infer_isize] skewness: 0.570; kurtosis: 0.230; ap_prior: 1.33e-04
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 3.06 sec
[bwa_sai2sam_pe_core] changing coordinates of 4990 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 10195 out of 12365 Q17 singletons are mated.
[bwa_paired_sw] 1265 out of 2897 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.52 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.57 sec
[bwa_sai2sam_pe_core] print alignments... 0.59 sec
[bwa_sai2sam_pe_core] 26458520 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.sai ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq
[main] Real time: 2762.464 sec; CPU: 1156.834 sec
[bam_sort_core] merging from 39 files...
Num 2
ID task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11
Name dedup_bam_PE_1 rep1
Thread thread_Root
PID 16002
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-06-02 12:01:52
End 2017-06-02 12:01:52
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam
Output files ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.filt.bam
Dependencies 
 
# SYS command. line 262

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 278

 if [[ 0 > 0 ]]; then \
                samtools view -F 524 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam | \
                sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam; \
                samtools view -h ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam | \
                $(which assign_multimappers.py) -k 0 --paired-end | \
                samtools fixmate -r /dev/stdin ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam.fixmate.bam; \
                else \
                    samtools view -F 1804 -f 2 -q 30 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam | \
                    sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam; \
                    samtools fixmate -r ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam.fixmate.bam; \
                fi

# SYS command. line 290

 samtools view -F 1804 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam.fixmate.bam | sambamba sort -t 1 /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.filt.bam

# SYS command. line 292

 rm -f ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 293

 rm -f ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam

# SYS command. line 295

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
 
    
--------------------Stderr--------------------
sambamba-sort: Unable to write to stream
ChIPSeq/chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11.sh: line 21: 19368 Broken pipe             samtools view -F 1804 -f 2 -q 30 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam
     19369 Segmentation fault      (core dumped) | sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /home/rdali/.bds/bds
string _LMFILES_ /sb/software/CentOS-6/tools/Modules/3.2.9/modulefiles/perl/5.16:/sb/software/CentOS-6/eb/modules/all/Core/Java/1.8.0_45.lua
string _ModuleTable001_ 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
string _ModuleTable002_ 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
string _ModuleTable003_ bC9MaW51eCIsIi9zYi9zb2Z0d2FyZS9DZW50T1MtNi9lYi9tb2R1bGVzL2FsbC9Db3JlIiwiL3NiL2hvbWUvcmRhbGkvbW9kdWxlZmlsZXMiLH0sWyJzeXN0ZW1CYXNlTVBBVEgiXT0iL3NiL3NvZnR3YXJlL0NlbnRPUy02L3Rvb2xzL01vZHVsZXMvMy4yLjkvbW9kdWxlZmlsZXM6L3NiL3NvZnR3YXJlL0NlbnRPUy02L2ViL21vZHVsZXMvYWxsL0xpbnV4Oi9zYi9zb2Z0d2FyZS9DZW50T1MtNi9lYi9tb2R1bGVzL2FsbC9Db3JlOi9zYi9ob21lL3JkYWxpL21vZHVsZWZpbGVzIixbInZlcnNpb24iXT0yLH0=
string _ModuleTable_Sz_ 3
bool allowEmpty false
string[] args [-title, 160130_CTCF, -final_stage, peak, -gensz, hs, -out_dir, ChIPSeq/160130_CTCF, -chrsz, tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes, -nth, 1, -type, TF, -species, hg19, -bwa_idx, tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa, -pe1, -fastq1_1:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq, -fastq1_2:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq, -ctl_pe1, -ctl_fastq1_1:1, HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq, -ctl_fastq1_2:1, HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq]
string BASH_ENV /software/CentOS-6/tools/lmod/lmod/init/bash
string BASH_FUNC_ml() () { eval $($LMOD_DIR/ml_cmd \"$@\")\n}
string BASH_FUNC_module() () { eval $($LMOD_CMD bash \"$@\");\n [ $? = 0 ] && eval $(${LMOD_SETTARG_CMD:-:} -s sh)\n}
bool canFail false
string CONDA_DEFAULT_ENV aquas_chipseq
string CONDA_PATH_BACKUP tools/miniconda3/bin:tools/perl5/bin:/software/CentOS-6/tools/perl-5.16/bin:/opt/torque/x86_64/bin:/usr/lib64/qt-3.3/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:tools:tools/cmake-3.4.1/bin:tools/circos-0.68/bin:tools/MACS-1.4.2/bin:tools/bam-readcount/build/bin:tools/HTSeq-0.6.1/scripts:tools/bowtie-1.1.1:tools/hicup_v0.5.3:/usr/bin/gnuplot:tools/hdf5-1.8.14/bin:/home/rdali/tools/pythonPackages/bin:/home/rdali/tools/pythonPackages:/home/rdali/tools/tabix-0.2.6:/home/rdali/tools/vcftools_0.1.12b/perl:/home/rdali/tools/samtools-0.1.19/bcftools:/home/rdali/tools/IGVTools:/home/rdali/tools/novocraft:/home/rdali/tools/bowtie2-2.1.0:/home/rdali/tools/tophat-2.0.11.Linux_x86_64:/home/rdali/tools/samtools-0.1.19:/home/rdali/.aspera/connect/bin:/home/rdali/tools/FastQC:/home/rdali/tools/cutadapt-1.4.1/bin:/home/rdali/tools:/home/rdali/software/bin:/home/rdali/tools/sratoolkit.2.3.5-2-centos_linux64/bin:/home/rdali/tools/bedtools-2.17.0/bin:/home/rdali/tools/bwa-0.7.10:/home/rdali/tools/mySoftwareLibs:/home/rdali/tools/ghostscript-9.15/bin:/home/rdali/tools/weblogo:tools/homer/bin:/sb/home/rdali/.local/lib/python2.7/site-packages:/home/rdali/.bds:/home/rdali/bin
string CONDA_PREFIX tools/miniconda3/envs/aquas_chipseq
string CONDA_PS1_BACKUP
string CPATH /software/CentOS-6/eb/software/Core/Java/1.8.0_45/include
int cpus -1
int cpusLocal 16
string CVS_RSH ssh
int day 86400
real E 2.718281828459045
string EBDEVELJAVA /software/CentOS-6/eb/software/Core/Java/1.8.0_45/easybuild/Core-Java-1.8.0_45-easybuild-devel
string EBROOTJAVA /software/CentOS-6/eb/software/Core/Java/1.8.0_45
string EBVERSIONJAVA 1.8.0_45
string ENVIRONMENT BATCH
int G 1073741824
string G_BROKEN_FILENAMES 1
string HDF5_DIR tools/hdf5-1.8.14/bin
string HISTCONTROL ignoreboth:erasedups
string HISTIGNORE ls:pwd:logout:rm*:mkdir*:rdali:hic:q
string HISTSIZE 1000000
string HISTTIMEFORMAT %F %T
string HOME /home/rdali
string HOSTNAME lm-4r10-n70
int hour 3600
string JAVA_HOME /software/CentOS-6/eb/software/Core/Java/1.8.0_45
int K 1024
string LANG C
string LD_LIBRARY_PATH /gs/software/CentOS-6/eb/software/Core/Java/1.8.0_45/jre/lib/amd64/server:/gs/software/CentOS-6/eb/software/Core/Java/1.8.0_45/jre/lib/amd64:/gs/software/CentOS-6/eb/software/Core/Java/1.8.0_45/jre/../lib/amd64:/software/CentOS-6/eb/software/Core/Java/1.8.0_45/lib:$LD_LIBRARY_PATH:~/software/lib:/home/rdali/software/lib:tools/hdf5-1.8.14/lib/:/home/rdali/tools/ghmm-0.9-rc3/lib:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/runtime/glnxa64:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/bin/glnxa64:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/server:~/software/lib:/home/rdali/software/lib:tools/hdf5-1.8.14/lib:/home/rdali/tools/ghmm-0.9-rc3/lib:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/runtime/glnxa64:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/bin/glnxa64:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/server
string LESSOPEN ||/usr/bin/lesspipe.sh %s
string LIBRARY_PATH /software/CentOS-6/eb/software/Core/Java/1.8.0_45/lib
string LMOD_arch x86_64
string LMOD_CMD /software/CentOS-6/tools/lmod/lmod/libexec/lmod
string LMOD_COLORIZE yes
string LMOD_DEFAULT_MODULEPATH /sb/software/CentOS-6/tools/Modules/3.2.9/modulefiles:/sb/software/CentOS-6/eb/modules/all/Linux:/sb/software/CentOS-6/eb/modules/all/Core:/sb/home/rdali/modulefiles
string LMOD_DIR /software/CentOS-6/tools/lmod/lmod/libexec
string LMOD_FULL_SETTARG_SUPPORT no
string LMOD_PKG /software/CentOS-6/tools/lmod/lmod
string LMOD_PREPEND_BLOCK normal
string LMOD_SETTARG_CMD :
string LMOD_sys Linux
string LMOD_VERSION 6.1
string LOADEDMODULES perl/5.16:Java/1.8.0_45
string LOGNAME rdali
string LSCRATCH /localscratch/91503356.gm-1r16-n04.guillimin.clumeq.ca
int M 1048576
string MAIL /var/spool/mail/rdali
string MANPATH /software/CentOS-6/eb/software/Core/Java/1.8.0_45/man:/software/CentOS-6/tools/perl-5.16/man:/software/CentOS-6/tools/lmod/lmod/share/man::
int mem -1
int minute 60
string MODULEPATH /sb/software/CentOS-6/tools/Modules/3.2.9/modulefiles:/sb/software/CentOS-6/eb/modules/all/Linux:/sb/software/CentOS-6/eb/modules/all/Core:/sb/home/rdali/modulefiles
string MODULEPATH_ROOT /sb/software/CentOS-6/eb/modules/all
string MODULESHOME /software/CentOS-6/tools/lmod/lmod
string NLSPATH /usr/dt/lib/nls/msg/%L/%N.cat
string node
int P 1125899906842624
string PATH /software/CentOS-6/eb/software/Core/Java/1.8.0_45:/software/CentOS-6/eb/software/Core/Java/1.8.0_45/bin:tools/miniconda3/envs/aquas_chipseq/extra/phantompeakqualtools:tools/miniconda3/envs/aquas_chipseq/bin:tools/miniconda3/bin:tools/perl5/bin:/software/CentOS-6/tools/perl-5.16/bin:/opt/torque/x86_64/bin:/usr/lib64/qt-3.3/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:tools:tools/cmake-3.4.1/bin:tools/circos-0.68/bin:tools/MACS-1.4.2/bin:tools/bam-readcount/build/bin:tools/HTSeq-0.6.1/scripts:tools/bowtie-1.1.1:tools/hicup_v0.5.3:/usr/bin/gnuplot:tools/hdf5-1.8.14/bin:/home/rdali/tools/pythonPackages/bin:/home/rdali/tools/pythonPackages:/home/rdali/tools/tabix-0.2.6:/home/rdali/tools/vcftools_0.1.12b/perl:/home/rdali/tools/samtools-0.1.19/bcftools:/home/rdali/tools/IGVTools:/home/rdali/tools/novocraft:/home/rdali/tools/bowtie2-2.1.0:/home/rdali/tools/tophat-2.0.11.Linux_x86_64:/home/rdali/tools/samtools-0.1.19:/home/rdali/.aspera/connect/bin:/home/rdali/tools/FastQC:/home/rdali/tools/cutadapt-1.4.1/bin:/home/rdali/tools:/home/rdali/software/bin:/home/rdali/tools/sratoolkit.2.3.5-2-centos_linux64/bin:/home/rdali/tools/bedtools-2.17.0/bin:/home/rdali/tools/bwa-0.7.10:/home/rdali/tools/mySoftwareLibs:/home/rdali/tools/ghostscript-9.15/bin:/home/rdali/tools/weblogo:tools/homer/bin:/sb/home/rdali/.local/lib/python2.7/site-packages:/home/rdali/.bds:/home/rdali/bin:tools/miniconda3/envs/aquas_chipseq/extra/align2rawsignal/bin
string PBS_ENVIRONMENT PBS_BATCH
string PBS_GPUFILE /var/spool/pbs/aux//91503356.gm-1r16-n04.guillimin.clumeq.cagpu
string PBS_JOBCOOKIE 9DEB57F6415F639D50503B9C2E3B4F29
string PBS_JOBID 91503356.gm-1r16-n04.guillimin.clumeq.ca
string PBS_JOBNAME AQUAS-160130_CTCF
string PBS_MICFILE /var/spool/pbs/aux//91503356.gm-1r16-n04.guillimin.clumeq.camic
string PBS_MOMPORT 15003
string PBS_NODEFILE /var/spool/pbs/aux//91503356.gm-1r16-n04.guillimin.clumeq.ca
string PBS_NODENUM 0
string PBS_NP 1
string PBS_NUM_NODES 1
string PBS_NUM_PPN 1
string PBS_O_HOME /home/rdali
string PBS_O_HOST lg-1r14-n04.guillimin.clumeq.ca
string PBS_O_LANG en_CA.UTF-8
string PBS_O_LOGNAME rdali
string PBS_O_MAIL /var/spool/mail/rdali
string PBS_O_PATH tools/miniconda3/bin:tools/perl5/bin:/software/CentOS-6/tools/perl-5.16/bin:/opt/torque/x86_64/bin:/usr/lib64/qt-3.3/bin:/opt/moab/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:/sb/software/tools/scripts:/usr/lpp/mmfs/bin:/usr/lpp/mmfs/bin:tools:tools/cmake-3.4.1/bin:tools/circos-0.68/bin:tools/MACS-1.4.2/bin:tools/bam-readcount/build/bin:tools/HTSeq-0.6.1/scripts:tools/bowtie-1.1.1:tools/hicup_v0.5.3:/usr/bin/gnuplot:tools/hdf5-1.8.14/bin:/home/rdali/tools/pythonPackages/bin:/home/rdali/tools/pythonPackages:/home/rdali/tools/tabix-0.2.6:/home/rdali/tools/vcftools_0.1.12b/perl:/home/rdali/tools/samtools-0.1.19/bcftools:/home/rdali/tools/IGVTools:/home/rdali/tools/novocraft:/home/rdali/tools/bowtie2-2.1.0:/home/rdali/tools/tophat-2.0.11.Linux_x86_64:/home/rdali/tools/samtools-0.1.19:/home/rdali/.aspera/connect/bin:/home/rdali/tools/FastQC:/home/rdali/tools/cutadapt-1.4.1/bin:/home/rdali/tools:/home/rdali/software/bin:/home/rdali/tools/sratoolkit.2.3.5-2-centos_linux64/bin:/home/rdali/tools/bedtools-2.17.0/bin:/home/rdali/tools/bwa-0.7.10:/home/rdali/tools/mySoftwareLibs:/home/rdali/tools/ghostscript-9.15/bin:/home/rdali/tools/weblogo:tools/homer/bin:/sb/home/rdali/.local/lib/python2.7/site-packages:/home/rdali/.bds:/home/rdali/bin
string PBS_O_QUEUE metaq
string PBS_O_SERVER gm-schrmat
string PBS_O_SHELL /bin/bash
string PBS_O_SUBMIT_FILTER /opt/torque/x86_64/libexec/qsub_filter
string PBS_O_WORKDIR ChIPSeq
string PBS_QUEUE xlm2
string PBS_TASKNUM 1
string PBS_VERSION TORQUE-5.1.3
string PBS_VNODENUM 0
string PBS_WALLTIME 86400
string PBSCOREDUMP 1
string PERL5LIB tools/perl5/lib/perl5:/home/rdali/tools/vcftools_0.1.12b/perl
string PERL_LOCAL_LIB_ROOT tools/perl5
string PERL_MB_OPT --install_base \"tools/perl5\"
string PERL_MM_OPT INSTALL_BASE=tools/perl5
real PI 3.141592653589793
string ppwd ChIPSeq
string programName chipseq.bds
string programPath tools/TF_chipseq_pipeline/chipseq.bds
string PROMPT_COMMAND history -a
string PWD ChIPSeq
string QTDIR /usr/lib64/qt-3.3
string QTINC /usr/lib64/qt-3.3/include
string QTLIB /usr/lib64/qt-3.3/lib
string queue
string R_LIBS tools/R_LIBS
string RAMDISK /dev/shm/91503356.gm-1r16-n04.guillimin.clumeq.ca
int retry 0
string SCRATCH /gs/scratch/rdali
string SHELL /bin/bash
string SHLVL 3
string SSH_ASKPASS /usr/libexec/openssh/gnome-ssh-askpass
string system local
int T 1099511627776
int timeout -1
string USER rdali
string VDB_PWFILE keys/prj_6419.ngc
int walltimeout 8640000
int week 604800
string XAPPLRESDIR tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/X11/app-defaults
string XFILESEARCHPATH /usr/dt/app-defaults/%L/Dt
leepc12 commented 7 years ago

This looks like sambamba issue (https://github.com/chapmanb/bcbio-nextgen/issues/1055). Did you have enough disk space on $TMP?

rdali commented 7 years ago

So disk space on $TMP certainly made a difference. I gave it 1TB and it ran for 4 days. The exit status in the STDOUT is 0 but it seems that macs2 had an error. How do I fix that? if I do not specify a peak caller, will both spp and macs2 be used? Also, what is the final output of the pipeline at the "peak" stage to know things are ok. I assume the "nodup.tagAlign.filt.regionPeak.gz" file is a good indication things are complete?

rdali commented 7 years ago
4 days 14:15:59.701 ExecutionerLocal 'Local[41]': Tasks [Local[41]] Pending: 0 Running: 1 Done: 26 Failed: 2 PID Task state Task name Dependencies Task definition
6644 running (RUNNING) macs2 n/s rep1-pr2 macs2 callpeak -t project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign.gz -c project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_17

Traceback (most recent call last): File "tools/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in import('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2') File ".local/lib/python2.7/site-packages/pkg_resources/init.py", line 719, in run_script self.require(requires)[0].run_script(script_name, ns) File ".local/lib/python2.7/site-packages/pkg_resources/init.py", line 1517, in run_script exec(script_code, namespace, namespace) File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in

File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 55, in main

File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 30, in File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 27, in File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 7, in File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 6, in bootstrap File "init.pxd", line 155, in init MACS2.IO.Parser (MACS2/IO/Parser.c:24419) ValueError: numpy.dtype has the wrong size, try recompiling Task failed: Program & line : 'tools/TF_chipseq_pipeline/modules/callpeak_macs2_chipseq.bds', line 83 Task Name : 'macs2 n/s rep1-pr2' Task ID : 'chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr2.line_83.id_36' Task PID : '6644' Task hint : 'macs2 callpeak -t project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign.gz -c project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_17' Task resources : 'cpus: -1 mem: -1.0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign.gz, project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.gz]' Output files : '[project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.narrowPeak.gz]' Script file : 'project/ChIPSeq/chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr2.line_83.id_36.sh' Exit status : '1' Program : 

    # SYS command. line 85

     if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

    # SYS command. line 86

     export LC_COLLATE=C

    # SYS command. line 91

     macs2 callpeak -t project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign.gz -c project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.gz -f BED -n project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 230 --keep-dup all -B --SPMR 

    # SYS command. line 94

     sort -k 8gr,8gr "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.narrowPeak.gz

    # SYS command. line 97

     rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_peaks.xls \
                "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_peaks.narrowPeak \
                "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_summits.bed

    # SYS command. line 101

     if [[ false == "false" ]]; then \
                rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg; \
                TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; \
                exit; \
            fi

    # SYS command. line 111

     macs2 bdgcmp -t "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg -c "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg --outdir project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2 -o "HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_FE.bdg -m FE

    # SYS command. line 114

     slopBed -i "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_FE.bdg -g tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bedgraph

    # SYS command. line 115

     rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_FE.bdg

    # SYS command. line 118

     sort -k1,1 -k2,2n project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bedgraph > project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.srt.bedgraph

    # SYS command. line 119

     bedGraphToBigWig project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.srt.bedgraph tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bw

    # SYS command. line 120

     rm -f project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bedgraph project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.srt.bedgraph

    # SYS command. line 126

     chipReads=$(zcat project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

    # SYS command. line 128

     controlReads=$(zcat project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

    # SYS command. line 130

     macs2 bdgcmp -t "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg -c "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg --outdir project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2 -o "HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

    # SYS command. line 133

     slopBed -i "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_ppois.bdg -g tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bedgraph

    # SYS command. line 134

     rm -rf "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_ppois.bdg

    # SYS command. line 137

     sort -k1,1 -k2,2n project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bedgraph > project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.srt.bedgraph

    # SYS command. line 138

     bedGraphToBigWig project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.srt.bedgraph tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bw

    # SYS command. line 139

     rm -f project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bedgraph project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.srt.bedgraph

    # SYS command. line 141

     rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg

    # SYS command. line 143

     TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
StdErr (100000000 lines)  :
    Traceback (most recent call last):
      File "tools/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in <module>
        __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
      File ".local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 719, in run_script
        self.require(requires)[0].run_script(script_name, ns)
      File ".local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1517, in run_script
        exec(script_code, namespace, namespace)
      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in <module>

      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 55, in main

      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 30, in <module>
      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 27, in <module>
      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 7, in <module>
      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 6, in __bootstrap__
      File "__init__.pxd", line 155, in init MACS2.IO.Parser (MACS2/IO/Parser.c:24419)
    ValueError: numpy.dtype has the wrong size, try recompiling

4 days 14:16:01.881 Wait: Task 'chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr2.line_83.id_36' finished. 4 days 14:16:01.881 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bam.bedpe_to_tag_ctl1.line_651.id_30, state: FINISHED 4 days 14:16:01.881 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bam.bedpe_to_tag_ctl1.line_651.id_30' finished. 4 days 14:16:01.881 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.align_bwa.bwa_sam_PE_rep1.line_181.id_12, state: FINISHED 4 days 14:16:01.881 Wait: Task 'chipseq.bds.20170604_153842_923/task.align_bwa.bwa_sam_PE_rep1.line_181.id_12' finished. 4 days 14:16:01.881 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_13, state: FINISHED 4 days 14:16:01.881 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_13' finished. 4 days 14:16:01.881 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_ctl1_2.line_111.id_23, state: FINISHED 4 days 14:16:01.881 Wait: Task 'chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_ctl1_2.line_111.id_23' finished. 4 days 14:16:01.881 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_rep1_2.line_111.id_11, state: FINISHED 4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_rep1_2.line_111.id_11' finished. 4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bam.bam_to_bedpe_rep1.line_613.id_17, state: FINISHED 4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bam.bam_to_bedpe_rep1.line_613.id_17' finished. 4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bed.spr_PE_rep1.line_180.id_20, state: FINISHED 4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bed.spr_PE_rep1.line_180.id_20' finished. 4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bam.dedup_bam_PE_2_rep1.line_323.id_15, state: FINISHED 4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bam.dedup_bam_PE_2_rep1.line_323.id_15' finished. 4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.callpeak_spp.spp_rep1_pr1.line_68.id_33, state: FINISHED 4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.callpeak_spp.spp_rep1_pr1.line_68.id_33' finished. 4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bam.dedup_bam_PE_2_ctl1.line_323.id_27, state: FINISHED 4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bam.dedup_bam_PE_2_ctl1.line_323.id_27' finished. 4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.callpeak_spp.spp_rep1_pr2.line_68.id_34, state: FINISHED 4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.callpeak_spp.spp_rep1_pr2.line_68.id_34' finished. 4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_ctl1_1.line_111.id_22, state: FINISHED 4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_ctl1_1.line_111.id_22' finished. 4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.align_bwa.bwa_sam_PE_ctl1.line_181.id_24, state: FINISHED 4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.align_bwa.bwa_sam_PE_ctl1.line_181.id_24' finished. 4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_xcor.subsample_bedpe2tag_rep1.line_85.id_19, state: FINISHED 4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_xcor.subsample_bedpe2tag_rep1.line_85.id_19' finished. 4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_rep1_1.line_111.id_10, state: FINISHED 4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_rep1_1.line_111.id_10' finished. 4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bam.bedpe_to_tag_rep1.line_651.id_18, state: FINISHED 4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bam.bedpe_to_tag_rep1.line_651.id_18' finished. 4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr1.line_83.id_35, state: ERROR Task failed: Program & line : 'tools/TF_chipseq_pipeline/modules/callpeak_macs2_chipseq.bds', line 83 Task Name : 'macs2 n/s rep1-pr1' Task ID : 'chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr1.line_83.id_35' Task PID : '4610' Task hint : 'macs2 callpeak -t project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign.gz -c project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_17' Task resources : 'cpus: -1 mem: -1.0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign.gz, project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.gz]' Output files : '[project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.narrowPeak.gz]' Script file : 'project/ChIPSeq/chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr1.line_83.id_35.sh' Exit status : '1' Program : 

    # SYS command. line 85

     if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

    # SYS command. line 86

     export LC_COLLATE=C

    # SYS command. line 91

     macs2 callpeak -t project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign.gz -c project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.gz -f BED -n project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 230 --keep-dup all -B --SPMR 

    # SYS command. line 94

     sort -k 8gr,8gr "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.narrowPeak.gz

    # SYS command. line 97

     rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_peaks.xls \
                "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_peaks.narrowPeak \
                "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_summits.bed

    # SYS command. line 101

     if [[ false == "false" ]]; then \
                rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg; \
                TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; \
                exit; \
            fi

    # SYS command. line 111

     macs2 bdgcmp -t "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg -c "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg --outdir project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1 -o "HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_FE.bdg -m FE

    # SYS command. line 114

     slopBed -i "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_FE.bdg -g tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bedgraph

    # SYS command. line 115

     rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_FE.bdg

    # SYS command. line 118

     sort -k1,1 -k2,2n project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bedgraph > project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.srt.bedgraph

    # SYS command. line 119

     bedGraphToBigWig project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.srt.bedgraph tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bw

    # SYS command. line 120

     rm -f project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bedgraph project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.srt.bedgraph

    # SYS command. line 126

     chipReads=$(zcat project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

    # SYS command. line 128

     controlReads=$(zcat project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

    # SYS command. line 130

     macs2 bdgcmp -t "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg -c "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg --outdir project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1 -o "HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

    # SYS command. line 133

     slopBed -i "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_ppois.bdg -g tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bedgraph

    # SYS command. line 134

     rm -rf "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_ppois.bdg

    # SYS command. line 137

     sort -k1,1 -k2,2n project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bedgraph > project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.srt.bedgraph

    # SYS command. line 138

     bedGraphToBigWig project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.srt.bedgraph tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bw

    # SYS command. line 139

     rm -f project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bedgraph project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.srt.bedgraph

    # SYS command. line 141

     rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg

    # SYS command. line 143

     TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
StdErr (100000000 lines)  :
    Traceback (most recent call last):
      File "tools/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in <module>
        __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
      File ".local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 719, in run_script
        self.require(requires)[0].run_script(script_name, ns)
      File ".local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1517, in run_script
        exec(script_code, namespace, namespace)
      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in <module>

      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 55, in main

      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 30, in <module>
      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 27, in <module>
      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 7, in <module>
      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 6, in __bootstrap__
      File "__init__.pxd", line 155, in init MACS2.IO.Parser (MACS2/IO/Parser.c:24419)
    ValueError: numpy.dtype has the wrong size, try recompiling

4 days 14:16:01.883 Wait: Task 'chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr1.line_83.id_35' finished. Fatal error: tools/TF_chipseq_pipeline/chipseq.bds, line 1237, pos 2. Task/s failed. chipseq.bds, line 76 : main() chipseq.bds, line 79 : void main() { // chipseq pipeline starts here chipseq.bds, line 91 : call_peaks() // call peaks in parallel (MACS2,SPP) chipseq.bds, line 820 : void call_peaks() { chipseq.bds, line 1237 : wait

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. 4 days 14:16:02.500 Writing report file 'chipseq.bds.20170604_153842_923.report.html' 4 days 14:16:02.634 Program 'chipseq.bds.20170604_153842_923' finished, exit value: 1, tasks executed: 27, tasks failed: 3, tasks failed names: macs2 n/s rep1 , macs2 n/s rep1-pr2 , macs2 n/s rep1-pr1. 4 days 14:16:02.635 Finished. Exit code: 1 4 days 14:16:02.635 ExecutionerLocal 'Local[41]': Killed 4 days 14:16:02.702 ExecutionerLocal 'Local[41]': Finished running

leepc12 commented 7 years ago

If a peak-caller is not specified, it defaults to spp. In such case, macs2 is used for generating bigwigs. Yes if you got nodup.tagAlign.filt.regionPeak.gz, then that means spp ran successfully.

About macs2 error, it looks like macs2 is combined with wrong numpy version. Please check the following:

$ source activate aquas_chipseq
$ conda list numpy
rdali commented 7 years ago

packages in environment at tools/miniconda3/envs/aquas_chipseq:

numpy 1.10.2 py27_0

leepc12 commented 7 years ago

It's a problem related to Conda's virtual environment. https://github.com/conda/conda/issues/448#issuecomment-195848539

Can you add the following to your ~/.bashrc and re-login?

export PYTHONNOUSERSITE=True

Please let me know if this works.

rdali commented 7 years ago

I get a different error now:

    INFO  @ Fri, 09 Jun 2017 15:33:37: #3   Write bedGraph files for control lambda (after scaling if necessary)... project/ChIPSeq/160130_CTCF/peak/macs2/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign_control_lambda.bdg 
    INFO  @ Fri, 09 Jun 2017 15:33:37: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
    INFO  @ Fri, 09 Jun 2017 15:33:37: #3 Call peaks for each chromosome... 
    Traceback (most recent call last):
      File "tools/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in <module>
        __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 744, in run_script
      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 1506, in run_script
      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in <module>

      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 56, in main

      File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 261, in run
      File "MACS2/PeakDetect.pyx", line 105, in MACS2.PeakDetect.PeakDetect.call_peaks (MACS2/PeakDetect.c:1632)
      File "MACS2/PeakDetect.pyx", line 251, in MACS2.PeakDetect.PeakDetect.__call_peaks_w_control (MACS2/PeakDetect.c:3172)
      File "MACS2/IO/CallPeakUnit.pyx", line 857, in MACS2.IO.CallPeakUnit.CallerFromAlignments.call_peaks (MACS2/IO/CallPeakUnit.c:12297)
      File "MACS2/IO/CallPeakUnit.pyx", line 911, in MACS2.IO.CallPeakUnit.CallerFromAlignments.call_peaks (MACS2/IO/CallPeakUnit.c:12049)
      File "MACS2/IO/CallPeakUnit.pyx", line 966, in MACS2.IO.CallPeakUnit.CallerFromAlignments.__chrom_call_peak_using_certain_criteria (MACS2/IO/CallPeakUnit.c:12455)
      File "MACS2/IO/CallPeakUnit.pyx", line 461, in MACS2.IO.CallPeakUnit.CallerFromAlignments.__pileup_treat_ctrl_a_chromosome (MACS2/IO/CallPeakUnit.c:6457)
    EOFError

00:38:10.137 Wait: Task 'chipseq.bds.20170609_152437_788/task.callpeak_macs2_chipseq.macs2_n_s_rep1.line_83.id_10' finished. Fatal error: tools/TF_chipseq_pipeline/chipseq.bds, line 1237, pos 2. Task/s failed. chipseq.bds, line 76 : main() chipseq.bds, line 79 : void main() { // chipseq pipeline starts here chipseq.bds, line 91 : call_peaks() // call peaks in parallel (MACS2,SPP) chipseq.bds, line 820 : void call_peaks() { chipseq.bds, line 1237 : wait

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. 00:38:10.377 Writing report file 'chipseq.bds.20170609_152437_788.report.html' 00:38:10.416 Program 'chipseq.bds.20170609_152437_788' finished, exit value: 1, tasks executed: 3, tasks failed: 2, tasks failed names: macs2 n/s rep1-pr1 , macs2 n/s rep1. 00:38:10.417 Finished. Exit code: 1 00:38:10.417 ExecutionerLocal 'Local[38]': Killed

leepc12 commented 7 years ago

https://github.com/taoliu/MACS/issues/105 Can you check your disk space on $TMP?

$ echo $TMP
$ df -h $TMP
rdali commented 7 years ago

$echo $TMP

$ df -h $TMP Filesystem Size Used Avail Use% Mounted on /dev/sda6 193G 42G 141G 23% / tmpfs 32G 149M 32G 1% /dev/shm /dev/sda2 477M 116M 337M 26% /boot /dev/sda1 200M 260K 200M 1% /boot/efi /dev/sda3 30G 20G 8.1G 72% /cvmfs-cache /dev/gs 3.1P 2.9P 221T 93% /gs /dev/lb 1.3P 1.1P 145T 89% /lb /dev/sb 456T 405T 52T 89% /sb /dev/sf1 349T 229T 120T 66% /sf1

I had set $TMPDIR to the extra 1TB not $TMP:

$echo $TMPDIR /gs/scratch/

$ df -h $TMPDIR Filesystem Size Used Avail Use% Mounted on /dev/gs 1.0T 2.0M 1.0T 1% /gs

leepc12 commented 7 years ago

Sorry. MACS2 does not use $TMP or $TMPDIR. It always writes temporary files on /tmp. Can you check your /tmp too?

rdali commented 7 years ago

df -h /tmp Filesystem Size Used Avail Use% Mounted on /dev/sda6 217G 19G 188G 9% /

leepc12 commented 7 years ago

I guess that your /tmp was running out of space at the moment you ran the pipeline. Can you try running pipelines again?

rdali commented 7 years ago

Looks like it ran to completion. Thanks!