leepc12
commented
6 years ago Did you run with -nth 32 (32 threads for the pipeline rune)? Do you have such cpus on your system? Do you also have enough disk space (>30G) and memory (>16G) on your system? Please post a full log.
$ df -h $ free -h
Thanks,
Jin
On Wed, Feb 7, 2018 at 7:40 AM, lpalomerol notifications@github.com wrote:
Hello,
this is my first time with this pipeline and I am got stucked launching this first one. Probably code must be ok, and the problem would be mine... but I cannot understand what is happening, because (until I can see) there is not specific trace.
Could you help me, please? I've been checking the cause during two days and I do not understand what is happening.
I would appreciate any help!
This is the launching trace:
`
== git info Latest git commit : a9389cb https://github.com/kundajelab/atac_dnase_pipelines/commit/a9389cb01c47c4479101f1963018515412a77166 (Thu Jan 11 04:23:30 2018) Reading parameters from section (default) in file(/home/idibell/Documentos/ pipelines/8.pujana/20180206.anne.atac/results/20180206. run.atacseq/../../../../../../opt/atac_dnase_pipelines/default.env)...
== configuration file info Hostname : lpalomero.idibelll.org Configuration file : Environment file : /home/idibell/Documentos/pipelines/8.pujana/20180206. anne.atac/results/20180206.run.atacseq/../../../../../../ opt/atac_dnase_pipelines/default.env
== parallelization info No parallel jobs : false Maximum # threads : 32
== 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 Java temporary directory : ${TMPDIR}
Info: Environments module not found on your system (e.g. /etc/profile.d/modules.sh). Ignoring shell env. parameters like '-mod'.
== shell environment info Conda env. : bds_atac Conda env. for python3 : bds_atac_py3 Conda bin. directory :
Shell cmd. for init. : if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi; export PATH=/home/idibell/Documentos/pipelines/8.pujana/20180206. anne.atac/results/20180206.run.atacseq/../../../../../../ opt/atac_dnase_pipelines/.:/home/idibell/Documentos/ pipelines/8.pujana/20180206.anne.atac/results/20180206. run.atacseq/../../../../../../opt/atac_dnase_pipelines/ modules:/home/idibell/Documentos/pipelines/8.pujana/ 20180206.anne.atac/results/20180206.run.atacseq/../../../ ../../../opt/atac_dnase_pipelines/utils:${PATH}:/bin:/ usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for init.(py3) : if [[ -f $(which conda) && $(conda env list | grep bds_atac_py3 | wc -l) != "0" ]]; then source activate bds_atac_py3; sleep 5; fi; export PATH=/home/idibell/Documentos/ pipelines/8.pujana/20180206.anne.atac/results/20180206. run.atacseq/../../../../../../opt/atac_dnase_pipelines/.:/ home/idibell/Documentos/pipelines/8.pujana/20180206. anne.atac/results/20180206.run.atacseq/../../../../../../ opt/atac_dnase_pipelines/modules:/home/idibell/ Documentos/pipelines/8.pujana/20180206.anne.atac/results/ 20180206.run.atacseq/../../../../../../opt/atacdnase pipelines/utils:${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)."; sleep 0
Cluster task min. len. : 60
Cluster task delay : 0
== output directory/title info Output dir. : /home/idibell/Documentos/pipelines/8.pujana/20180206. anne.atac/results/20180206.run.atacseq/out Title (prefix) : 20180206.run.atacseq Reading parameters from section (default) in file(/home/idibell/Documentos/ pipelines/8.pujana/20180206.anne.atac/results/20180206. run.atacseq/../../../../../../opt/atac_dnase_pipelines/default.env)... Reading parameters from section (hg38) in file(/home/idibell/Documentos/ data/genome/bds_atac_species.conf)...
== species settings Species : hg38 Species file : /home/idibell/Documentos/data/genome/bds_atac_species.conf
Species name (WashU browser) : hg38 Ref. genome seq. fasta : /home/idibell/Documentos/data/ genome/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta Chr. sizes file : /home/idibell/Documentos/data/ genome/hg38/hg38.chrom.sizes Black list bed : /home/idibell/Documentos/data/genome/hg38/hg38.blacklist. 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 ENCODE alias suffix :
== report settings URL root for output directory : Genome coord. for browser tracks :
== align multimapping settings alignments reported for multimapping : 0
== align bowtie2 settings Bowtie2 index : /home/idibell/Documentos/data/genome/hg38/bowtie2_index/ GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta Replacement --score-min for bowtie2 : Walltime (bowtie2) : 47h Max. memory (bowtie2) : 12G Extra param. (bowtie2) :
== adapter trimmer settings Maximum allowed error rate for cutadapt : 0.10 Minimum trim. length for cutadapt -m : 5 Walltime (adapter trimming) : 23h Max. memory (adapter trimming) : 12G
== postalign bam settings MAPQ reads rm thresh. : 30 Rm. tag reads with str. : chrM 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 : Max. memory for cross-corr. analysis : 15G
== callpeak macs2 settings Genome size (hs,mm) : hs Walltime (macs2) : 23h Max. memory (macs2) : 15G Cap number of peaks (macs2) : 300K Extra parameters for macs2 callpeak :
== callpeak naiver overlap settings Bedtools intersect -nonamecheck : false
== IDR settings Append IDR threshold to IDR out_dir : false
== ATAQC settings TSS enrichment bed : /home/idibell/Documentos/data/genome/hg38/ataqc/hg38_ gencode_tss_unique.bed.gz DNase bed for ataqc : /home/idibell/Documentos/data/ genome/hg38/ataqc/reg2map_honeybadger2_dnase_allp10 ucsc.hg19_to_hg38.bed.gz Promoter bed for ataqc : /home/idibell/Documentos/data/ genome/hg38/ataqc/reg2map_honeybadger2_dnase_prom_p2.hg19_to_hg38.bed.gz Enhancer bed for ataqc : /home/idibell/Documentos/data/ genome/hg38/ataqc/reg2map_honeybadger2_dnase_enh_p2.hg19_to_hg38.bed.gz Reg2map for ataqc : /home/idibell/Documentos/data/ genome/hg38/ataqc/hg38_dnase_avg_fseq_signal_formatted.txt.gz Reg2map_bed for ataqc : /home/idibell/Documentos/data/ genome/hg38/ataqc/hg38_celltype_compare_subsample.bed.gz Roadmap metadata for ataqc : /home/idibell/Documentos/data/ genome/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt Max. memory for ATAQC : 20G Walltime for ATAQC : 47h
== atac pipeline settings Type of pipeline : atac-seq Align only : false reads to subsample replicates (0 if no subsampling) : 0 reads to subsample for cross-corr. analysis : 25000000
No pseudo replicates : false No ATAQC (advanced QC report) : false No Cross-corr. analysis : false Use CSEM for alignment : false Smoothing window for MACS2 : 150 DNase Seq : false IDR threshold : 0.1 Force to use ENCODE3 parameter set : false Force to use ENCODE parameter set : false Disable genome browser tracks : false p-val thresh. for overlapped peaks : 0.01 MACS2 p-val thresh. for peaks : 0.01 MACS2 p-val thresh. for BIGWIGs : 0.01 Enable IDR on called peaks : false Automatically find/trim adapters : false
== checking atac parameters ...
Checking parameters and data files for ATAQC.
== checking adapters to be trimmed ... Rep1 R1 adapters (PE) : 00: no adapter specified. Rep1 R2 adapters (PE) : 00: no adapter specified.
== checking input files ...
Rep1 fastq (PE) : /home/idibell/Documentos/pipelines/8.pujana/20180206. anne.atac/results/20180206.run.atacseq/../../../../../ data/datasets/fastq.hakemann/468_plus_Crisper_169_S7_L002_R1_001.fastq.gz /home/idibell/Documentos/pipelines/8.pujana/20180206. anne.atac/results/20180206.run.atacseq/../../../../../ data/datasets/fastq.hakemann/468_plus_Crisper_S8_L002_R1_001.fastq.gz Distributing 32 to ...
`
And here is the error trace:
`
Task failed: Program & line : '../../../../../../opt/atac_ dnase_pipelines/modules/align_bowtie2.bds', line 144 Task Name : 'bowtie2_PE rep1' Task ID : 'atac.bds.20180207_150019_769_parallel41/task.align bowtie2.bowtie2_PE_rep1.line_144.id_10' Task PID : '6837' Task hint : 'bowtie2 -X2000 --mm --local --threads 32 -x /home/idibell/Documentos/data/genome/hg38/bowtie2_index/ GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta; -1 /home/idibell/Documentos/pipelines/8.pujana/20180206. anne.atac/results/20180206.run.atacseq/../../../../../ data/datasets/fastq.hakemann/468_plu' Task resources : 'cpus: 32 mem: -1,0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[/home/idibell/Documentos/pipelines/8.pujana/20180206. anne.atac/results/20180206.run.atacseq/../../../../../ data/datasets/fastq.hakemann/468_plus_Crisper_169_S7_L002_R1_001.fastq.gz, /home/idibell/Documentos/pipelines/8.pujana/20180206. anne.atac/results/20180206.run.atacseq/../../../../../ data/datasets/fastq.hakemann/468_plus_Crisper_S8_L002_R1_001.fastq.gz]' Output files : '[/home/idibell/Documentos/pipelines/8.pujana/20180206. anne.atac/results/20180206.run.atacseq/out/align/rep1/ 468_plus_Crisper_169_S7_L002_R1_001.PE2SE.bam, /home/idibell/Documentos/ pipelines/8.pujana/20180206.anne.atac/results/20180206. run.atacseq/out/qc/rep1/468_plus_Crisper_169_S7_L002R1 001.PE2SE.align.log]' Script file : '/home/idibell/Documentos/pipelines/8.pujana/20180206. anne.atac/results/20180206.run.atacseq/atac.bds.20180207_ 150019_769_parallel_41/task.align_bowtie2.bowtie2_PE_rep1. line_144.id_10.sh' Exit status : '1' Program :
# SYS command. line 146 if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi; export PATH=/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../../opt/atac_dnase_pipelines/.:/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../../opt/atac_dnase_pipelines/modules:/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../../opt/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s) # SYS command. line 151 bowtie2 -X2000 --mm --local --threads 32 -x /home/idibell/Documentos/data/genome/hg38/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta \ -1 /home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../data/datasets/fastq.hakemann/468_plus_Crisper_169_S7_L002_R1_001.fastq.gz -2 /home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../data/datasets/fastq.hakemann/468_plus_Crisper_S8_L002_R1_001.fastq.gz 2>/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/out/qc/rep1/468_plus_Crisper_169_S7_L002_R1_001.PE2SE.align.log | \ samtools view -Su /dev/stdin | samtools sort - /home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/out/align/rep1/468_plus_Crisper_169_S7_L002_R1_001.PE2SE # SYS command. line 154 cat /home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/out/qc/rep1/468_plus_Crisper_169_S7_L002_R1_001.PE2SE.align.log # SYS command. line 155 samtools index /home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/out/align/rep1/468_plus_Crisper_169_S7_L002_R1_001.PE2SE.bam # SYS command. line 157 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0 StdErr (100000000 lines) : [bam_sort_core] merging from 49 files...Fatal error: ../../../../../../opt/atac_dnase_pipelines/atac.bds, line 789, pos 3. Task/s failed.
Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. Fatal error: ../../../../../../opt/atac_dnase_pipelines/atac.bds, line 426, pos 2. Task/s failed.
Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. `
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lpalomerol
Hello,
this is my first time with this pipeline and I am got stucked launching this first one. Probably code must be ok, and the problem would be mine... but I cannot understand what is happening, because (until I can see) there is not specific trace.
Could you help me, please? I've been checking the cause during two days and I do not understand what is happening.
I would appreciate any help!
This is the launching trace:
`
== git info Latest git commit : a9389cb01c47c4479101f1963018515412a77166 (Thu Jan 11 04:23:30 2018) Reading parameters from section (default) in file(/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../../opt/atac_dnase_pipelines/default.env)...
== configuration file info Hostname : lpalomero.idibelll.org Configuration file : Environment file : /home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../../opt/atac_dnase_pipelines/default.env
== parallelization info No parallel jobs : false Maximum # threads : 32
== 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 Java temporary directory : ${TMPDIR}
Info: Environments module not found on your system (e.g. /etc/profile.d/modules.sh). Ignoring shell env. parameters like '-mod'.
== shell environment info Conda env. : bds_atac Conda env. for python3 : bds_atac_py3 Conda bin. directory :
Shell cmd. for init. : if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi; export PATH=/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../../opt/atac_dnase_pipelines/.:/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../../opt/atac_dnase_pipelines/modules:/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../../opt/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for init.(py3) : if [[ -f $(which conda) && $(conda env list | grep bds_atac_py3 | wc -l) != "0" ]]; then source activate bds_atac_py3; sleep 5; fi; export PATH=/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../../opt/atac_dnase_pipelines/.:/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../../opt/atac_dnase_pipelines/modules:/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../../opt/atac_dnase_pipelines/utils:${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)."; sleep 0
Cluster task min. len. : 60
Cluster task delay : 0
== output directory/title info Output dir. : /home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/out Title (prefix) : 20180206.run.atacseq Reading parameters from section (default) in file(/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../../opt/atac_dnase_pipelines/default.env)... Reading parameters from section (hg38) in file(/home/idibell/Documentos/data/genome/bds_atac_species.conf)...
== species settings Species : hg38 Species file : /home/idibell/Documentos/data/genome/bds_atac_species.conf
Species name (WashU browser) : hg38 Ref. genome seq. fasta : /home/idibell/Documentos/data/genome/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta Chr. sizes file : /home/idibell/Documentos/data/genome/hg38/hg38.chrom.sizes Black list bed : /home/idibell/Documentos/data/genome/hg38/hg38.blacklist.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 ENCODE alias suffix :
== report settings URL root for output directory : Genome coord. for browser tracks :
== align multimapping settings
alignments reported for multimapping : 0
== align bowtie2 settings Bowtie2 index : /home/idibell/Documentos/data/genome/hg38/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta Replacement --score-min for bowtie2 : Walltime (bowtie2) : 47h Max. memory (bowtie2) : 12G Extra param. (bowtie2) :
== adapter trimmer settings Maximum allowed error rate for cutadapt : 0.10 Minimum trim. length for cutadapt -m : 5 Walltime (adapter trimming) : 23h Max. memory (adapter trimming) : 12G
== postalign bam settings MAPQ reads rm thresh. : 30 Rm. tag reads with str. : chrM 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 : Max. memory for cross-corr. analysis : 15G
== callpeak macs2 settings Genome size (hs,mm) : hs Walltime (macs2) : 23h Max. memory (macs2) : 15G Cap number of peaks (macs2) : 300K Extra parameters for macs2 callpeak :
== callpeak naiver overlap settings Bedtools intersect -nonamecheck : false
== IDR settings Append IDR threshold to IDR out_dir : false
== ATAQC settings TSS enrichment bed : /home/idibell/Documentos/data/genome/hg38/ataqc/hg38_gencode_tss_unique.bed.gz DNase bed for ataqc : /home/idibell/Documentos/data/genome/hg38/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.hg19_to_hg38.bed.gz Promoter bed for ataqc : /home/idibell/Documentos/data/genome/hg38/ataqc/reg2map_honeybadger2_dnase_prom_p2.hg19_to_hg38.bed.gz Enhancer bed for ataqc : /home/idibell/Documentos/data/genome/hg38/ataqc/reg2map_honeybadger2_dnase_enh_p2.hg19_to_hg38.bed.gz Reg2map for ataqc : /home/idibell/Documentos/data/genome/hg38/ataqc/hg38_dnase_avg_fseq_signal_formatted.txt.gz Reg2map_bed for ataqc : /home/idibell/Documentos/data/genome/hg38/ataqc/hg38_celltype_compare_subsample.bed.gz Roadmap metadata for ataqc : /home/idibell/Documentos/data/genome/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt Max. memory for ATAQC : 20G Walltime for ATAQC : 47h
== atac pipeline settings Type of pipeline : atac-seq Align only : false
reads to subsample replicates (0 if no subsampling) : 0
reads to subsample for cross-corr. analysis : 25000000
No pseudo replicates : false No ATAQC (advanced QC report) : false No Cross-corr. analysis : false Use CSEM for alignment : false Smoothing window for MACS2 : 150 DNase Seq : false IDR threshold : 0.1 Force to use ENCODE3 parameter set : false Force to use ENCODE parameter set : false Disable genome browser tracks : false p-val thresh. for overlapped peaks : 0.01 MACS2 p-val thresh. for peaks : 0.01 MACS2 p-val thresh. for BIGWIGs : 0.01 Enable IDR on called peaks : false Automatically find/trim adapters : false
== checking atac parameters ...
Checking parameters and data files for ATAQC.
== checking adapters to be trimmed ... Rep1 R1 adapters (PE) : 00: no adapter specified. Rep1 R2 adapters (PE) : 00: no adapter specified.
== checking input files ...
Rep1 fastq (PE) : /home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../data/datasets/fastq.hakemann/468_plus_Crisper_169_S7_L002_R1_001.fastq.gz /home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../data/datasets/fastq.hakemann/468_plus_Crisper_S8_L002_R1_001.fastq.gz Distributing 32 to ...
`
And here is the error trace:
`
Task failed: Program & line : '../../../../../../opt/atac_dnase_pipelines/modules/align_bowtie2.bds', line 144 Task Name : 'bowtie2_PE rep1' Task ID : 'atac.bds.20180207_150019_769_parallel_41/task.align_bowtie2.bowtie2_PE_rep1.line_144.id_10' Task PID : '6837' Task hint : 'bowtie2 -X2000 --mm --local --threads 32 -x /home/idibell/Documentos/data/genome/hg38/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta; -1 /home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../data/datasets/fastq.hakemann/468_plu' Task resources : 'cpus: 32 mem: -1,0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../data/datasets/fastq.hakemann/468_plus_Crisper_169_S7_L002_R1_001.fastq.gz, /home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/../../../../../data/datasets/fastq.hakemann/468_plus_Crisper_S8_L002_R1_001.fastq.gz]' Output files : '[/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/out/align/rep1/468_plus_Crisper_169_S7_L002_R1_001.PE2SE.bam, /home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/out/qc/rep1/468_plus_Crisper_169_S7_L002_R1_001.PE2SE.align.log]' Script file : '/home/idibell/Documentos/pipelines/8.pujana/20180206.anne.atac/results/20180206.run.atacseq/atac.bds.20180207_150019_769_parallel_41/task.align_bowtie2.bowtie2_PE_rep1.line_144.id_10.sh' Exit status : '1' Program :
Fatal error: ../../../../../../opt/atac_dnase_pipelines/atac.bds, line 789, pos 3. Task/s failed.
Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. Fatal error: ../../../../../../opt/atac_dnase_pipelines/atac.bds, line 426, pos 2. Task/s failed.
Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. `