Hello I'm trying to run unzip using the conda package using ccs reads as input. I had no problem running falcon but when I run unzip I get a samtools help menu rather than unzip output.
Program: samtools (Tools for alignments in the SAM format)
Version: 1.8 (using htslib 1.8)
Usage: samtools [options]
Commands:
-- Indexing
dict create a sequence dictionary file
faidx index/extract FASTA
index index alignment
-- Editing
calmd recalculate MD/NM tags and '=' bases
fixmate fix mate information
reheader replace BAM header
targetcut cut fosmid regions (for fosmid pool only)
addreplacerg adds or replaces RG tags
markdup mark duplicates
-- File operations
collate shuffle and group alignments by name
cat concatenate BAMs
merge merge sorted alignments
mpileup multi-way pileup
sort sort alignment file
split splits a file by read group
quickcheck quickly check if SAM/BAM/CRAM file appears intact
fastq converts a BAM to a FASTQ
fasta converts a BAM to a FASTA
-- Statistics
bedcov read depth per BED region
depth compute the depth
flagstat simple stats
idxstats BAM index stats
phase phase heterozygotes
stats generate stats (former bamcheck)
-- Viewing
flags explain BAM flags
tview text alignment viewer
view SAM<->BAM<->CRAM conversion
depad convert padded BAM to unpadded BAM
2019-05-23 00:03:45,157 - falcon_unzip.io:54http://falcon_unzip.io:54 - INFO - samtools ['1', '8'] is >= 1.3
2019-05-23 00:03:45,157 - root:145 - INFO - CD: '0-rawreads' <- '/global/projectb/scratch/aclum/sequel_II/PB1179/falcon_preads/2-asm-falcon'
aclum
commented
5 years ago
Hello I'm trying to run unzip using the conda package using ccs reads as input. I had no problem running falcon but when I run unzip I get a samtools help menu rather than unzip output.
Version info: ./fc_unzip.py -h falcon-unzip 1.2.0 (pip thinks "falcon-unzip 1.2.0") falcon-kit 1.3.0 pypeflow 2.2.0
Below is the log.
qaqc) aclum@dint06:/projectb/scratch/aclum/sequel_II/PB1179/falcon_preads/2-asm-falcon> more all.log 2019-05-23 00:03:43,198 - fc_run:552 - INFO - Setup logging from file "None". 2019-05-23 00:03:43,203 - fc_run:126 - INFO - Using config= {'General': {}, 'Unzip': {'input_fofn': 'input_preads.fofn', 'polish_include_zmw_all_subreads': False, 'polish_use_blasr': False, 'polish_vc_ignore_error': False}, 'job.defaults': {'MB': '192000', 'NPROC': '24', 'max_n_open_files': '150', 'njobs': '10', 'pwatcher_type': 'blocking', 'submit': 'sbatch --wait -C haswell -A fnglasmb --qos=genepool_special -J ${JOB_NAME} -o ${JOB_STDOUT} -e ${JOB_STDERR} -N 1 --e 'use_tmpdir': False}, 'job.step.unzip.blasr_aln': {'MB': '32000', 'NPROC': '4', 'njobs': '45'}, 'job.step.unzip.hasm': {'MB': '512000', 'NPROC': '64', 'njobs': '1'}, 'job.step.unzip.phasing': {'MB': '192000', 'NPROC': '24', 'njobs': '10'}, 'job.step.unzip.quiver': {'MB': '192000', 'NPROC': '24', 'njobs': '50'}, 'job.step.unzip.track_reads': {'MB': '512000', 'NPROC': '64', 'njobs': '20'}, 'max_n_open_files': 300} 2019-05-23 00:03:43,214 - falcon_unzip.io:69http://falcon_unzip.io:69 - INFO - PATH=/usr/common/jgi/oracle_client/11.2.0.3.0/client_1/bin:/global/projectb/sandbox/rqc/qc_us /gaag/aclum/pb_falcon_conda_cori/bin:/usr/common/software/jamo/prod/bin:/usr/common/software/python/2.7-anaconda-4.4/bin:/usr/common/software/pytho n:/usr/common/software/darshan/3.1.4/bin:/usr/common/software/altd/2.0/bin:/usr/common/software/bin:/usr/common/mss/bin:/usr/common/nsg/bin:/opt/gc /2.2.18-6.0.7.1_5.47g2aa4f39.ari/bin:/opt/cray/alps/6.6.43-6.0.7.1_5.45__ga796da32.ari/sbin:/opt/cray/job/2.2.3-6.0.7.1_5.43g6c4e934.ari/bin:/o braries_2018.1.163/linux/bin/intel64:/opt/ovis/bin:/opt/ovis/sbin:/usr/syscom/nsg/sbin:/usr/syscom/nsg/bin:/opt/cray/pe/modules/3.2.10.6/bin:/globahttp://3.2.10.6/bin:/globa n/X11:/usr/games:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/cray/pe/bin 2019-05-23 00:03:43,215 - root:23 - INFO - $('which which') 2019-05-23 00:03:43,225 - root:31 - DEBUG - Call 'which which' returned 0. 2019-05-23 00:03:43,225 - root:23 - INFO - $('which blasr') 2019-05-23 00:03:43,241 - root:31 - DEBUG - Call 'which blasr' returned 0. 2019-05-23 00:03:43,241 - root:23 - INFO - $('which samtools') 2019-05-23 00:03:43,260 - root:31 - DEBUG - Call 'which samtools' returned 0. 2019-05-23 00:03:43,260 - root:23 - INFO - $('which pbalign') 2019-05-23 00:03:43,276 - root:31 - DEBUG - Call 'which pbalign' returned 0. 2019-05-23 00:03:43,276 - root:23 - INFO - $('which gcpp') 2019-05-23 00:03:43,294 - root:31 - DEBUG - Call 'which gcpp' returned 0. 2019-05-23 00:03:43,294 - root:23 - INFO - $('which minimap2') 2019-05-23 00:03:43,333 - root:31 - DEBUG - Call 'which minimap2' returned 0. 2019-05-23 00:03:43,333 - root:23 - INFO - $('which nucmer') 2019-05-23 00:03:43,377 - root:31 - DEBUG - Call 'which nucmer' returned 0. 2019-05-23 00:03:43,378 - root:23 - INFO - $('which show-coords') 2019-05-23 00:03:43,390 - root:31 - DEBUG - Call 'which show-coords' returned 0. 2019-05-23 00:03:43,391 - root:23 - INFO - $('which fc_rr_hctg_track2.exe') 2019-05-23 00:03:43,405 - root:31 - DEBUG - Call 'which fc_rr_hctg_track2.exe' returned 0. 2019-05-23 00:03:43,406 - root:23 - INFO - $('nucmer --version') 2019-05-23 00:03:44,455 - root:31 - DEBUG - Call 'nucmer --version' returned 0. 2019-05-23 00:03:44,455 - root:23 - INFO - $('minimap2 --version') 2019-05-23 00:03:44,483 - root:31 - DEBUG - Call 'minimap2 --version' returned 0. 2019-05-23 00:03:44,484 - root:23 - INFO - $('racon --version') 2019-05-23 00:03:44,583 - root:31 - DEBUG - Call 'racon --version' returned 0. 2019-05-23 00:03:44,584 - root:43 - INFO - $ show-coords -h > 2019-05-23 00:03:44,664 - root:43 - INFO - $ samtools > 2019-05-23 00:03:45,156 - root:50 - DEBUG - 1 <- 'samtools':
Program: samtools (Tools for alignments in the SAM format) Version: 1.8 (using htslib 1.8)
Usage: samtools [options]
Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA index index alignment
-- Editing calmd recalculate MD/NM tags and '=' bases fixmate fix mate information reheader replace BAM header targetcut cut fosmid regions (for fosmid pool only) addreplacerg adds or replaces RG tags markdup mark duplicates
-- File operations collate shuffle and group alignments by name cat concatenate BAMs merge merge sorted alignments mpileup multi-way pileup sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA
-- Statistics bedcov read depth per BED region depth compute the depth flagstat simple stats idxstats BAM index stats phase phase heterozygotes stats generate stats (former bamcheck)
-- Viewing flags explain BAM flags tview text alignment viewer view SAM<->BAM<->CRAM conversion depad convert padded BAM to unpadded BAM
2019-05-23 00:03:45,157 - falcon_unzip.io:54http://falcon_unzip.io:54 - INFO - samtools ['1', '8'] is >= 1.3 2019-05-23 00:03:45,157 - root:145 - INFO - CD: '0-rawreads' <- '/global/projectb/scratch/aclum/sequel_II/PB1179/falcon_preads/2-asm-falcon'