Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Issue with Chip-seq pipeline: jobid: 27: one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode! #939

Closed
Jerolen opened this issue Dec 7, 2022 · 8 comments · Fixed by #940
Closed

Issue with Chip-seq pipeline: jobid: 27: one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode! #939

Jerolen opened this issue Dec 7, 2022 · 8 comments · Fixed by #940
Labels
question Further information is requested

Comments

@Jerolen
Copy link

Jerolen commented Dec 7, 2022

Question
Hi There, I am trying to test out the chip-set pipeline using a single sample of paired end data but the workflow keeps failing at a specific point with the following error:

Activating conda environment: ../opt/miniconda3/envs/seq2science/lib/python3.8/site-packages/seq2science/.snakemake/6824310427e127c1e8fdddc2f1df8a12
/bin/bash: line 1: shuf: command not found
[Wed Dec 7 15:20:57 2022]
Error in rule random_subset_peaks:
jobid: 27
output: /Users/jerolen/my_project2/results/qc/computeMatrix_peak/GRCh38-macs2_N20000.bed
conda-env: /Users/jerolen/opt/miniconda3/envs/seq2science/lib/python3.8/site-packages/seq2science/.snakemake/6824310427e127c1e8fdddc2f1df8a12
shell:

    shuf -n 20000 /Users/jerolen/my_project2/results/macs2/GRCh38_combinedsummits.bed | bedtools slop -i stdin -g /Users/jerolen/my_project2/genomes/GRCh38/GRCh38.fa.sizes -b 1000 > /Users/jerolen/my_project2/results/qc/computeMatrix_peak/GRCh38-macs2_N20000.bed
    
    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

What have I tried
I have tried changing the alignment tool from bwa to hisat2 with no luck. Any advice would be greatly appreciated as I am completely out of depth on the coding side of things. config.yaml, samples.tsv and export of terminal attached. Thank you.

config-yaml.txt
samples.txt
Terminal Saved Output-Jerolen-Seq2SCience-chipseq.txt
@Jerolen Jerolen added the question Further information is requested label Dec 7, 2022
@Jerolen Jerolen changed the title Issue with Chip-set pipeline: jobid: 27: one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode! Issue with Chip-seq pipeline: jobid: 27: one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode! Dec 7, 2022
@Maarten-vd-Sande
Copy link
Member

Thanks for the issue! I think there's actually a problem on "our" side here. Seems like we haven't defined the environment properly and we are making use of the shuf command which isn't by default on all systems (e.g. on a mac)...

Let me take a look!

For now you can turn off the deeptools figures for the QC report as this is purely used for visualization only. In the config.yaml add:

deeptools_qc: false

@Maarten-vd-Sande
Copy link
Member

Maarten-vd-Sande commented Dec 7, 2022 •
edited
Loading

I don't have a mac, so you will have to check for me if this solution fixes it 😄

This file should already exists:

/opt/miniconda3/envs/seq2science/lib/python3.8/site-packages/seq2science/envs/bedtools.yaml

Can you change it so that it has coreutils added:

name: bedtools
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - bioconda::bedtools=2.29.2
  - conda-forge::coreutils=9.1
  - conda-forge::conda-ecosystem-user-package-isolation=1.0

And then try seq2science again? Seq2science should automatically detect the environment definition has been changed and will re-install the environment.

@Maarten-vd-Sande Maarten-vd-Sande linked a pull request Dec 7, 2022 that will close this issue
update bedtools env; fixes #939 #940
Merged
4 tasks
@Jerolen
Copy link
Author

Jerolen commented Dec 7, 2022 via email

@Maarten-vd-Sande
Copy link
Member

Have you had the time to test if this works?

@Jerolen
Copy link
Author

Jerolen commented Dec 14, 2022 via email

@Maarten-vd-Sande
Copy link
Member

Not sure, 16GB isn't too much indeed for preprocessing.. Which step(s) is the one crashing? Still the random_subset_peaks rule? Most rules make a logfile, perhaps there is a clue about what goes wrong?

https://vanheeringen-lab.github.io/seq2science/content/faq.html#one-of-the-rules-failed-and-the-log-turns-red

@Maarten-vd-Sande Maarten-vd-Sande mentioned this issue Dec 22, 2022
Closed
@Maarten-vd-Sande
Copy link
Member

Your issue(s) should be solved with the latest 0.9.7 release. Let me know if you encounter anything else!!!

@Jerolen
Copy link
Author

Jerolen commented Jan 17, 2023 via email

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
question Further information is requested
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

update bedtools env; fixes #939 vanheeringen-lab/seq2science
2 participants
@Maarten-vd-Sande @Jerolen