search

mikewolfe / ChIPseq_pipeline

A general ChIP-seq pipeline to reproducibly process many samples at once.
0 stars 3 forks source link

Issue with development pipeline branch, cmartt peak calling #18

Closed cmhustmyer closed 3 years ago

cmhustmyer commented 3 years ago

Hi Mike,

Just re-downloaded the pipeline and ran the test on the master branch, it works great. I cleaned all cores, then I switched to the development side of the pipeline, ran the test again, and got this error towards the end. Seems similar to the error a few months ago and I think might have to do with bowtie? Or I typed something incorrectly, thanks.

` 91 of 119 steps (76%) done [Tue May 25 11:10:38 2021] Error in rule cmarrt_call_peaks: jobid: 2 output: results/peak_calling/cmarrt/genotypeA_rep1_ext_median_log2ratioRZ.narrowPeak log: results/peak_calling/logs/cmarrt/genotypeA_rep1_ext_median_log2ratioRZ_cmarrt.log, results/peak_calling/logs/cmarrt/genotypeA_rep1_ext_median_log2ratioRZ_cmarrt.err (check log file(s) for error message) conda-env: /mnt/scratch/hustmyer/ChIPseq_pipeline/.snakemake/conda/b58f5225 shell: python3 workflow/CMARRT_python/run_cmarrt_bigwig.py results/coverage_and_norm/deeptools_log2ratio/genotypeA_rep1_ext_median_log2ratioRZ.bw 25 - o results/peak_calling/cmarrt/genotypeA_rep1_ext_median_log2ratioRZ --resolution 5 --consolidate 10 --plots > results/peak_calling/logs/cmarrt/genotypeA_rep1_ext_median_log2ratioRZ_cmarrt.log 2> results/peak_calling/logs/cmarrt/genotypeA_rep1_ext_median_log2ratioRZ_cmarrt.err (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Tue May 25 11:10:38 2021] Error in rule cmarrt_call_peaks: jobid: 3 output: results/peak_calling/cmarrt/genotypeA_rep2_ext_median_log2ratioRZ.narrowPeak log: results/peak_calling/logs/cmarrt/genotypeA_rep2_ext_median_log2ratioRZ_cmarrt.log, results/peak_calling/logs/cmarrt/genotypeA_rep2_ext_median_log2ratioRZ_cmarrt.err (check log file(s) for error message) conda-env: /mnt/scratch/hustmyer/ChIPseq_pipeline/.snakemake/conda/b58f5225 shell: python3 workflow/CMARRT_python/run_cmarrt_bigwig.py results/coverage_and_norm/deeptools_log2ratio/genotypeA_rep2_ext_median_log2ratioRZ.bw 25 - o results/peak_calling/cmarrt/genotypeA_rep2_ext_median_log2ratioRZ --resolution 5 --consolidate 10 --plots > results/peak_calling/logs/cmarrt/genotypeA_rep2_ext_median_log2ratioRZ_cmarrt.log 2> results/peak_calling/logs/cmarrt/genotypeA_rep2_ext_median_log2ratioRZ_cmarrt.err (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Tue May 25 11:10:38 2021] Finished job 75. 92 of 119 steps (77%) done [Tue May 25 11:10:40 2021] Finished job 8. 93 of 119 steps (78%) done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /mnt/scratch/hustmyer/ChIPseq_pipeline/.snakemake/log/2021-05-25T110829.598144.snakemake.log `

mikewolfe commented 3 years ago

This is an issue with the dependent CMARRT repository being on different commits between the branches. When checking out the development branch do the following:

git checkout develop
git submodule update

The git submodule update command will switch the commit of the CMARRT repository to be in lock step with develop. When switching back to the master branch be sure to call the git submodule update again. I.e.

git checkout master
git submodule update

This will no longer be an issue when develop is next merged into master.