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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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Trying to execute an non executable script #693

Closed gkanogiannis closed 11 months ago

gkanogiannis commented 1 year ago

Hi BRAKER developers,

In sub run_augustus_jobs of braker.pl, various augustus bash scripts are run by system("$cmdString"). These bash script files have been previously generated by createAugustusJoblist.pl and haven been given executable permissions with system("chmod +x $jobname").

Unfortunately in some file systems, the executable bit is not set and these files remain without exec rights and hence run_augustus_jobs fails at that point (loine 7684 of braker.pl in this case). Most probably there are other points where system("$cmdString") will fail.

As a workaround, I replaced system("$cmdString") with system("bash $cmdString"), unless you have another proposal or workaround.

Best regards,

Anestis

KatharinaHoff commented 11 months ago

Thank you for the suggestion. I have addressed it in commit https://github.com/Gaius-Augustus/BRAKER/commit/7729e4f288d5ef7b0f53106c40366cbd861b388e (currently in a branch, but soon merged to master)