Entering edit mode
23 days ago
marco.barr
▴
150
Hello everyone, I am running a complex pipeline on fastq files with a Perl script. At some point in the output, I get this strange error that I have never seen before in this analysis.
/home/MitoSAlt/bin/last-1542/bin/lastal: can't open file: tmp_MT10617M_S6.fq
Fri May 24 14:56:24 2024: Generate Bigwig
needLargeMem: trying to allocate 0 bytes (limit: 100000000000)
Use of uninitialized value $elements[6] in pattern match (m//) at MitoSAlt1.1.1_mod.pl line 221,
<CONFIG> line 64.
This is my command
perl MitoSAlt1.1.1_mod.pl config_human.txt file_R1.fastq file_R2.fastq sample_name
It's probably due to the fact that I receive an empty file as input? I don't understand how to fix it. I ran the same pipeline a few minutes ago on other samples, without making any changes to the Perl script, and everything worked fine. Maybe it's the samples? I ran it both on a slurm cluster and on a login node. And always the same error. Thank you very much for your help.
A quick search suggests the problem is your empty input file? See https://biostar.galaxyproject.org/p/6794
I managed to correct and solve the problem. It was due to issues with memory parameter settings on different login nodes. Additionally, I had mistakenly left a hyphen on a line of the script. Thank you very much anyway.