tmp files deleted before job is finished

[JuliaLopezDelgado]

Hello. I am trying to run the following code in a SGE script: HG-CoLoR --longreads $long_reads --shortreads $short_reads --tmpdir ./tmp --out HGCcor_long_reads.fasta --nproc 48

I get the following error, which I think happens because the temporary files are deleted before processing is complete: Traceback (most recent call last): File "/home/home02/bsjld/.conda/envs/genomeassembly/bin/filterShortReads.py", line 7, in <module> f = open(sys.argv[1]) FileNotFoundError: [Errno 2] No such file or directory: './tmp/quorum_corrected.fa' sed: can't read ./tmp/RC_long_quorum_corrected.fa: No such file or directory cat: ./tmp/RC_long_quorum_corrected.fa: No such file or directory mv: cannot stat ‘./tmp/good_long_quorum_corrected.fa’: No such file or directory /home/home02/bsjld/.conda/envs/genomeassembly/bin/HG-CoLoR: line 217: 130788 Floating point exception(core dumped) PgSAgen_hgcolor $tmpdir/"$k-mers-$SR" $tmpdir/"$k-mers-$SR" >> HG-CoLoR.stdout 2>> HG-CoLoR.stderr Traceback (most recent call last): File "/home/home02/bsjld/.conda/envs/genomeassembly/bin/filterOutShortAlignments.py", line 36, in <module> out.write(finalString) NameError: name 'out' is not defined Could you please help me with this issue? Thank you in advance.

[morispi]

Hey,

It seems like you are using a conda installed version of HG-CoLoR. Unfortunately, I do not maintain the conda version myself.

Could you please try to clone and install HG-CoLoR from the github repo? This should resolve your problem.

Can you keep me updated?

Cheers, Pierre

[JuliaLopezDelgado]

Hello, Sorry for the late reply! I re-installed it from the github repo instead of conda, and removed the .fasta from the resultPrefix and it works fine now. Thank you, Julia