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. [https://res.spikenow.com/c/?id=05pf9ntcrlo9tm3v&s=48&m=c&_ts=1r8w5y] 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 <robjsarg...@gmail.com<mailto:robjsarg...@gmail.com>> 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? [https://bolt.im/t/?x3f-xvIb3Jnnq-K7ZzpW8OqbpSIVkTyzMsVcmUwIYdY8cOq4aRxSh1Qx_OnXohoN2Tx6PEWZ8fh7AR1mV51fMA]
GEMMA_transformation_a1.jobs
Description: GEMMA_transformation_a1.jobs
