sort: unrecognized option

[narsapuramvijaykumar]

Hello Team,

I have recently come across this tool SwiftOrtho and installed in my local machine.
While running the find_ortho.py I had faced a small issue which I had fixed myself, but little unsure that it might effect speed or performance of the tool.

My command
$python SwiftOrtho/bin/find_orth.py -i examples/ref.fsa.sc -c 0.5 -y 0 > input.fsa.sc.orth

ERROR
sort: unrecognized option '--parallel=4'
Try `sort --help' for more information.
Traceback (most recent call last):
File "find_orth.py", line 446, in
f = open(qotsrt, 'r')
IOError: [Errno 2] No such file or directory: 'qry.fsa.sc.qOTs.txt.srt'

I had removed "--parallel" argument from sort command which is used in find_orth.py script
and re-run the pipeline, It had ran without any issue for time being.
But I would like to get confirmation regarding the effect of changes I had done and any suggest if there any other alternative solution to it.

Thanks & Regards,
Vijay N

[idoerg]

Hi Vijay,

Thanks for using SwiftOrtho, and for your feedback. Which OS have you installed this on? The Linux sort command has --parallel=N for number of sorts run concurrently, so I would be interested to know which OS does not have the --parallel. If you removed this argument you probably slowed down things.

Iddo

[narsapuramvijaykumar]

I use Red Hat Enterprise Linux Server release 6.9 (Santiago).

-Vijay N

[idoerg]

I use Red Hat Enterprise Linux Server release 6.9 (Santiago).

-Vijay N

Interesting. According to this:https://opensource.com/article/18/5/gnu-parallel sort may not have a --parallel option in some distros, probably becasue of an old version of GNU coreutils. Since sort is part of GNU coreutils, maybe you can install your own? https://www.gnu.org/software/coreutils/manual/html_node/index.html#Top

[narsapuramvijaykumar]

Ok @idoerg , Thanks for your inputs.

-Vijay N