pipeline failed in atac.filter #359
Comments
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Did you install pipeline's conda environment ( |
Yes， as I mentioned, I install pipeline's conda environment by running scripts/install_conda_env.sh and run with capper run ... --conda. |
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I have met the same problem as you. Have you solved this problem yet? @w111zsj |
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Please try this for debugging: $ source activate encode-atac-seq-pipeline # or conda activte
(encode-atac-seq-pipeline) $ conda env list
# conda environments:
#
base /users/leepc12/miniconda3
encode-atac-seq-pipeline * /users/leepc12/miniconda3/envs/encode-atac-seq-pipeline
encode-atac-seq-pipeline-macs2 /users/leepc12/miniconda3/envs/encode-atac-seq-pipeline-macs2
encode-atac-seq-pipeline-python2 /users/leepc12/miniconda3/envs/encode-atac-seq-pipeline-python2
encode-atac-seq-pipeline-spp /users/leepc12/miniconda3/envs/encode-atac-seq-pipeline-spp
(encode-atac-seq-pipeline) $ which python
/users/leepc12/miniconda3/envs/encode-atac-seq-pipeline/bin/python
(encode-atac-seq-pipeline) $ python --version
Python 3.6.6 :: Anaconda, Inc.
(encode-atac-seq-pipeline) $ which samtools
/users/leepc12/miniconda3/envs/encode-atac-seq-pipeline/bin/samtools
(encode-atac-seq-pipeline) $ samtools --version
samtools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd. |
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I'm person number 3 with this problem. I debugged as you suggested above and everything looks fine to me. |
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This looks like a bug in the pipeline. # cd to the git repo
$ cd atac-seq-pipeline
# edit the first line of src/assign_multimappers.py , replace python2 with python3
$ vi src/assign_multimappers.py
# then the python script should look like this
$ head src/assign_multimappers.py
#!/usr/bin/env python3
# piped script to take multimappers and randomly assign
# requires a qname sorted file!!
import sys
import random
import argparse
# transfer that python script to conda envs
$ scripts/update_conda_env.shPlease let me know if this fix works. |
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Worked like a charm for me. Thank you! |
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Closing this, I will make a new release today. |
and others
Describe the bug
Hi team,
My pipeline failed before entering the atac.filter step.
My caper was installed in conda environment (canu) so I ran this pipeline when activate canu.
caper run /home/zhaosj/software/encode_atacseq/atac-seq-pipeline/atac.wdl -i /home/zhaosj/proj/yeastatac/data/jasondb2015.json --conda canu
Conda environments corresponding to this pipeline were installed follow your instructions by running install_conda_env.sh.
Softlink (ln -s ) and hardlink (ln) work good in my filesystem.
Could you please help me fix this problem?
Many thanks,
Jason
OS/Platform
Caper configuration file
Paste contents of
~/.caper/default.conf.Input JSON file
Paste contents of your input JSON file.
{ "atac.title" : "JasonDB2015", "atac.description" : "This is the wt yeast ATACseq data from JasonDB etal Genome Research 2015.", "atac.pipeline_type" : "atac", "atac.align_only" : false, "atac.true_rep_only" : false, "atac.genome_tsv" : "/home/zhaosj/proj/yeastatac/ref/R64.tsv", "atac.paired_end" : true, "atac.fastqs_rep1_R1" : [ "/home/zhaosj/proj/yeastatac/data/lin2a_1.fastq.gz", "/home/zhaosj/proj/yeastatac/data/lin2b_1.fastq.gz", "/home/zhaosj/proj/yeastatac/data/lin2c_1.fastq.gz" ], "atac.fastqs_rep1_R2" : [ "/home/zhaosj/proj/yeastatac/data/lin2a_2.fastq.gz", "/home/zhaosj/proj/yeastatac/data/lin2b_2.fastq.gz", "/home/zhaosj/proj/yeastatac/data/lin2c_2.fastq.gz" ], "atac.fastqs_rep2_R1" : [ "/home/zhaosj/proj/yeastatac/data/lin3a_1.fastq.gz", "/home/zhaosj/proj/yeastatac/data/lin3b_1.fastq.gz", "/home/zhaosj/proj/yeastatac/data/lin3c_1.fastq.gz" ], "atac.fastqs_rep2_R2" : [ "/home/zhaosj/proj/yeastatac/data/lin3a_2.fastq.gz", "/home/zhaosj/proj/yeastatac/data/lin3b_2.fastq.gz", "/home/zhaosj/proj/yeastatac/data/lin3c_2.fastq.gz" ], "atac.fastqs_rep3_R1" : [ "/home/zhaosj/proj/yeastatac/data/lin6a_1.fastq.gz", "/home/zhaosj/proj/yeastatac/data/lin6b_1.fastq.gz", "/home/zhaosj/proj/yeastatac/data/lin6c_1.fastq.gz" ], "atac.fastqs_rep3_R2" : [ "/home/zhaosj/proj/yeastatac/data/lin6a_2.fastq.gz", "/home/zhaosj/proj/yeastatac/data/lin6b_2.fastq.gz", "/home/zhaosj/proj/yeastatac/data/lin6c_2.fastq.gz" ], "atac.auto_detect_adapter" : true, "atac.multimapping" : 4 }Troubleshooting result
If you ran
caper runwithout Caper server then Caper automatically runs a troubleshooter for failed workflows. Find troubleshooting result in the bottom of Caper's screen log.If you ran
caper submitwith a running Caper server then first find your workflow ID (1st column) withcaper listand runcaper debug [WORKFLOW_ID].Paste troubleshooting result.
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