Re: Properly setting $Global::max_file_length to avoid line 12170 error

[Rob Sargent]

On 10/4/22 23:12, Nagle, Michael F wrote:

No, I'm not using backslash continuation lines. I ctrl-F'd for backslashes and see none in my jobs file passed to parallel -a

Please find attached that jobs file. Perhaps it could provide some clue. However, the same format and script used to prepare it worked in Ubuntu 20.04 LTS and it's only now that I'm using 22.04 LTS that I'm having this problem.

    That's quite interesting.  I see no unreasonably long paths in the
    job file you sent.  Some step in the process might be quoting the
    entire line (or at least the arg list).
    
    I take it your "$job_list_name" might be the name of the file you
    sent?

Michael Nagle

Michael Nagle

PhD Candidate, Molecular and Cellular Biology

Forest Biotechnology Laboratory

Oregon State University

301-974-7221 (cell)

On October 5, 2022 at 4:44 GMT, Rob Sargent <robjsargent@gmail.com> wrote:

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On 10/4/22 22:33, Nagle, Michael F wrote:

Rob Sargent

[This email originated from outside of OSU. Use caution with links and attachments.]

The backslashes appear to be coming from parallel. My command has file paths with forward slashes and these are replaced with \_ by parallel, it seems.

To demonstrate, here is one my first command in the a I pass to parallel:
gemma -bfile ./1323_cohort_maf01_geno10.snp.pass -p ./pheno_files/callus_regeneration_PC1-uv_unique_rmoutliers_boxcox_resid.noheader.pheno -k ./1323_cohort_maf01_geno10.cXX.txt -lmm 1 -n 3 -miss 0.1 -o callus_regeneration_PC1-uv_unique_rmoutliers_boxcox_resid-ResidOverPhase

Here is the error for that command:
mkdir output/1/gemma -bfile .\_1323_cohort_maf01_geno10.snp.pass -p .\_pheno_files\_callus_regeneration_PC1-uv_unique_rmoutliers_boxcox_resid.noheader.pheno -k .\_1323_cohort_maf01_geno10.cXX.txt -lmm 1 -n 3 -miss 0.1 -o callus_regeneration_PC1-uv_unique_rmoutliers_boxc: Invalid argument at /home/gmobot/anaconda3/envs/gemma/bin/parallel line 12170.

Are you using backslash continuation lines by any chance?

_