perl Error - needLargeMem Bigwig
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.
• 1,261 views
•
link
written
by
marco.barr •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Initialization of MySQL (MariaDb) for Funannotate.
written by SomeOne •
-
Error Scaffolding with RagTag
written by Bipin •
-
Can I trust this script I wrote for assembling plant genomes?
written by breri •
-
Help scaffolding an Illumina genome assembly with 10x reads
written by maxwhjohn1988
-
Can HISAT2 be invoked in bash shell, and can it be fed variables or names with wildcards as inputs?
written by RNAseqer
-
Error: Snakemake skiped a rule
written by c.clarido
-
BWA mem running extremely slow
written by berge2015
-
A5 pipeline begin and end
written by Anand Rao
-
Forum: Parsing in perl - separate output to two files
written by eric.oswald •
-
Questions about using the Celera Genome Assembler for HGAP
written by tptacek3050
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.