CALLMAFFT.pl with --qsub 1

[TorHou]

Hello,

i found a small problem when I used CALLMAFFT in the reprocess mode with --qsub 1. When the number of regions in files_to_reprocess file is smaller than the $chunkSize then the calculation of my $n_chunks = ceil($n_files / $chunkSize); leads to $n_chunks being 1. This in turn means, that the -J parameter for the submission script is set to 1-1 and that is not allowed and this error is the result: qsub: illegal -J value

So probably it would be a good idea to check whether the number of files to process is smaller than $chunkSize and submit a job array only if necessary.

[evanbiederstedt]

Hi @TorHou

So probably it would be a good idea to check whether the number of files to process is smaller than $chunkSize and submit a job array only if necessary.

Good point!

I think this is a quick addition to the perl script. If you made a PR, we'll add that feature in.

Thanks, Evan

[TorHou]

Hi Evan,
if my Perl skills were any better I would have done that ;)
but yeah, next time I'll run into this problem I'll fix it.

[evanbiederstedt]

Hey @TorHou

"if my Perl skills were any better I would have done that ;)"

The PI for the Manchot-Group Dilthey would be the gentleman to ask here ;)

Sounds good! Whenever you have a chance, let's create a PR and we'll have a review