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error exit status (127) #24

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Jiseon623 opened this issue Apr 13, 2020 · 8 comments
Open

error exit status (127) #24

Jiseon623 opened this issue Apr 13, 2020 · 8 comments

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@Jiseon623
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Hello,
I tried using cegwas2-nf and it doesn't even go through the first process.
I tried to find the cause of this issue, but couldn't find it.

I attach the output when running the command NXF_VER=19.07.0 nextflow main.nf --traitfile=test_traits/PC1.tsv --vcf=bin/WI.20180527.impute.vcf.gz --p3d=TRUE --sthresh=BF:

Thank you in advance for your help

N E X T F L O W ~ version 19.07.0
Launching main.nf [confident_northcutt] - revision: 0a592c2713

C. elegans GWAS pipeline

Phenotype Directory = null
VCF = bin/WI.20180527.impute.vcf.gz
CeNDR Release = 20180527
P3D = true
Significance Threshold = BF
Max AF for Burden Mapping = 0.05
Min Strains with Variant for Burden = 2
Significance Threshold = BF
Gene File = bin/gene_ref_flat.Rda
Result Directory = Analysis_Results-20200413
Eigen Memory allocation = 100 GB

executor > local (1)
[e4/6cd3a3] process > fix_strain_names_bulk (BULK TRAIT) [ 0%] 0 of 1
[- ] process > vcf_to_geno_matrix -
[- ] process > chrom_eigen_variants -
[- ] process > collect_eigen_variants -
[- ] process > rrblup_maps -
[- ] process > summarize_maps -
[- ] process > prep_ld_files -
[- ] process > rrblup_fine_maps -
[- ] process > concatenate_LD_per_trait -
[- ] process > plot_genes -
[- ] process > burden_mapping -
[- ] process > plot_burden -
Error executing process > 'fix_strain_names_bulk (BULK TRAIT)'

Caused by:
Process fix_strain_names_bulk (BULK TRAIT) terminated with an error exit status (127)

Command executed:

Rscript --vanilla which Fix_Isotype_names_bulk.R PC1.tsv fix

Command exit status:
127

Command output:
(empty)

Command wrapper:
.command.run: line 202: module: command not found

Work dir:
/home/jiseon623/cegwas2-nf/work/e4/6cd3a3c66367217e09020d751dcfdb

executor > local (1)
[e4/6cd3a3] process > fix_strain_names_bulk (BULK TRAIT) [100%] 1 of 1, failed: 1 ✘
[- ] process > vcf_to_geno_matrix -
[- ] process > chrom_eigen_variants -
[- ] process > collect_eigen_variants -
[- ] process > rrblup_maps -
[- ] process > summarize_maps -
[- ] process > prep_ld_files -
[- ] process > rrblup_fine_maps -
[- ] process > concatenate_LD_per_trait -
[- ] process > plot_genes -
[- ] process > burden_mapping -
[- ] process > plot_burden -
Error executing process > 'fix_strain_names_bulk (BULK TRAIT)'

Caused by:
Process fix_strain_names_bulk (BULK TRAIT) terminated with an error exit status (127)

Command executed:

Rscript --vanilla which Fix_Isotype_names_bulk.R PC1.tsv fix

Command exit status:
127

Command output:
(empty)

Command wrapper:
.command.run: line 202: module: command not found

Work dir:
/home/jiseon623/cegwas2-nf/work/e4/6cd3a3c66367217e09020d751dcfdb

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
Failed to invoke workflow.onComplete event handler

-- Check script 'main.nf' at line: 773 or see '.nextflow.log' file for more details
@Thatguy027
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Hi,

The main error seems to be module: command not found

Are you running this from a computer or a cluster?

Can you please attach the .nextflow.log file, which might have more information.

Thanks

@Jiseon623
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Jiseon623 commented Apr 14, 2020 via email

@Thatguy027
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I think this might be a platform issue because we made this pipeline on a Linux cluster. It looks like you are running on a Linux computer, which we have not tested the pipeline on. I am not sure how different the personal Linux computer is from the cluster.

Here are some things I can recommend:

  1. Have you verified that Nextflow works on your system? Nextflow has a test after install that you can run to verify it is all working smoothly. See here

  2. If you found that Nextflow is successfully working on your machine: go to the directory that the pipeline failed: /home/jiseon623/cegwas2-nf/work/09/194f45d74a0f318a891e5615bd3045 and attempt to run the command outside of Nextflow. This can be done by running the following command in the above directory:

Rscript --vanilla path/to/this/file/Fix_Isotype_names_bulk.R data.tsv fix

  1. Finally, I think an old lab member of mine set up a docker container tagging him here: @faithman that might work more robustly on your personal machine. Here is the link

Let me know what happens when you try these things because it will help us make the pipeline better.

@Jiseon623
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Jiseon623 commented Apr 20, 2020 via email

@Thatguy027
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Hi again and sorry for the delays.

It looks like something has changed since your original post.. as you have made it further through the pipeline, which is indicated by:

[16/224a95] process > fix_strain_names_bulk (BULK TRAIT) [100%] 1 of 1 ✔
[fd/2dbaf6] process > vcf_to_geno_matrix (1)             [100%] 1 of 1 ✔
[4c/02c8c7] process > chrom_eigen_variants (IV)          [100%] 6 of 6 ✔
[fc/2f34be] process > collect_eigen_variants             [100%] 1 of 1 ✔
[68/4a79d2] process > rrblup_maps (m2)                   [100%] 2 of 2 ✔
[64/782952] process > summarize_maps                     [100%] 1 of 1,
failed: 1 ✘
[-        ] process > prep_ld_files                      -
[-        ] process > rrblup_fine_maps                   -
[-        ] process > concatenate_LD_per_trait           -
[-        ] process > plot_genes                         -
[9d/aaf905] process > burden_mapping (m2)                [100%] 2 of 2 ✔
[e7/c51ddb] process > plot_burden (m2)                   [100%] 2 of 2 ✔

I am curious to know what changed?

Regarding the current error, I am wondering if a significant QTL was identified by the mapping pipeline. I can't recall if I included a "Terminate pipeline if no significant QTL were identified" in the script. This might explain the current issue.

A couple of things to look for:

Check out the plots that are output in the Mappings/Plots folder, are any above the horizontal significance threshold line? Are there any pxgplot.pdf files, which would suggest a significant QTL. If the answer to these questions is no, then you can try lowering the significance threshold using the --sthresh=EIGEN flag when executing the nextflow pipeline. This threshold is usually between 4-5 on the y axis of the manhattan plot, so if some markers are above that, you should identify marginally significant QTL using the --sthresh=EIGEN flag.

If the answer is yes a significant QTL was identified but the pipeline still failed, then I would suggest entering the /home/jiseon623/test/work/64/7829520b2799e5432b5b4eee571481 directory where the pipeline failed and try executing the commands as last time to see if they work with on your current machine.

Please let me know how this troubleshooting goes, as we are gearing up to revamp this entire workflow

Thanks for your patience and your help!

@Jiseon623
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Jiseon623 commented Apr 27, 2020 via email

@Thatguy027
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Interesting...

At this point it seems like the issue is at a post-mapping processing step.

It will be difficult for me to offer more suggestions without doing some troubleshooting of my own.

Usually no output pxgplot.pdf means there were no significant QTL detected. This might make sense that the pipeline is crashing on the summarize mapping step if there are no QTL above the BF threshold. But you mentioned there are red dots in the manhattan plot so I am confused about that. If QTL above threshold are detected should also see blue regions surrounding each QTL that correspond to genomic regions that are processed further. If you do not see these in your manhattan plot, try running the pipeline again with --sthresh=EIGEN, which will lower the threshold for post-mapping QTL processing. Note that you can also add the -resume flag so you don't have to run the steps that already completed.

If this is not the issue, please let me know what files are in the summarize mapping directory and if you would be willing to share your data so I can see what the issue is.

@Jiseon623
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Jiseon623 commented Apr 29, 2020 via email

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@Thatguy027 @Jiseon623