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*
<https://spikenow.com/r/a/?ref=spike-organic-signature&_ts=1r8w5y>
1r8w5y
Michael Nagle
PhD Candidate, Molecular and Cellular Biology
Forest Biotechnology Laboratory
<http://people.forestry.oregonstate.edu/steve-strauss/home-page>
Oregon State University
301-974-7221 (cell)
On October 5, 2022 at 4:44 GMT, Rob Sargent <[email protected]> wrote:
[This email originated from outside of OSU. Use caution with links
and attachments.]
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?
_
