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langmead-lab / monorail-external

examples to run monorail externally
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Recount unify step failing for the rule "split_fianl_rejoined_exons" #19

Closed mayank-singh-sikarwar closed 2 years ago

mayank-singh-sikarwar commented 2 years ago

Run command: /bin/bash /nfs/home/users/msikarwa/Documents/monorail-external/singularity/run_recount_unify.sh \ /nfs/home/users/msikarwa/Documents/singularity/recount-unify_1.1.0.sif \ hg38 \ /nfs/home/users/msikarwa/Documents/reference \ /nfs/home/users/msikarwa/Documents/run_3/unify_out \ /nfs/home/users/msikarwa/Documents/run_3/pump_out/output/ \ /nfs/home/users/msikarwa/Documents/input_data/sample_file.tsv \ 6 \ SRP:237

Step failed with the below error(small snap of the session, full logs are in the attachment):

[Mon Jul 11 14:45:19 2022] rule split_final_rejoined_exons: input: all.exon_counts.rejoined.tsv.gz, all.exon_counts.rejoined.tsv.gz.accession_header output: exon_sums_per_study/37/SRP020237/mre.exon_sums.SRP020237.G026.gz, exon_sums_per_study/37/SRP020237/mre.exon_sums.SRP020237.G029.gz, exon_sums_per_study/37/SRP020237/mre.exon_sums.SRP020237.R109.gz, exon_sums_per_study/37/SRP020237/mre.exon_sums.SRP020237.F006.gz, exon_sums_per_study/37/SRP020237/mre.exon_sums.SRP020237.ERCC.gz, exon_sums_per_study/37/SRP020237/mre.exon_sums.SRP020237.SIRV.gz jobid: 19 threads: 6

    /bin/bash /recount-unify/rejoin/split_out_exon_sums_by_study.sh mre G026,G029,R109,F006,ERCC,SIRV 1709834 /container-mounts/ref/exon_bitmasks.tsv /container-mounts/ref/exon_bitmask_coords.tsv all.exon_counts.rejoined.tsv.gz 6
    rm -rf exons_split_by_study_temp exon_annotation_split_runs

SRP020237 no_runs ls: cannot access 'exons_split_by_study_temp/*.gz': No such file or directory [Mon Jul 11 14:45:19 2022] Error in rule split_final_rejoined_exons: jobid: 19 output: exon_sums_per_study/37/SRP020237/mre.exon_sums.SRP020237.G026.gz, exon_sums_per_study/37/SRP020237/mre.exon_sums.SRP020237.G029.gz, exon_sums_per_study/37/SRP020237/mre.exon_sums.SRP020237.R109.gz, exon_sums_per_study/37/SRP020237/mre.exon_sums.SRP020237.F006.gz, exon_sums_per_study/37/SRP020237/mre.exon_sums.SRP020237.ERCC.gz, exon_sums_per_study/37/SRP020237/mre.exon_sums.SRP020237.SIRV.gz

RuleException: CalledProcessError in line 333 of /recount-unify/Snakefile: Command ' set -euo pipefail;
/bin/bash /recount-unify/rejoin/split_out_exon_sums_by_study.sh mre G026,G029,R109,F006,ERCC,SIRV 1709834 /container-mounts/ref/exon_bitmasks.tsv /container-mounts/ref/exon_bitmask_coords.tsv all.exon_counts.rejoined.tsv.gz 6 rm -rf exons_split_by_study_temp exon_annotation_split_runs ' returned non-zero exit status 2. File "/recount-unify/Snakefile", line 333, in __rule_split_final_rejoined_exons File "/opt/conda/envs/recount-unify/lib/python3.9/concurrent/futures/thread.py", line 52, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /container-mounts/working/.snakemake/log/2022-07-11T144342.634057.snakemake.log

Comment: I am following all the instructions given in the readme docs and keeping each steps output separate to avoid any mix. I am using the latest image for both steps and latest fastQ files for this test run. However, I am not able to pinpoint why this error occurred. Please direct me how I can resolve this issue. Also, let me know if you need any other details from my side. run_log.txt monorail_commands.txt