Error in STEP 1 - 01.run_all_assemblies.pl.

jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis

GNU General Public License v3.0

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Error in STEP 1 - 01.run_all_assemblies.pl. #780

Closed Manso002 closed 5 months ago

Manso002 commented 5 months ago

Hello, I just started my very first run on squeezemeta and it failed on step 1. I have seen other issues posted here and I am not sure if it is a memory problem. I am running with 128gB RAM memory and 1.4TB free disk space. I've attached syslog file and megahit file as well.

log.file.zip syslog.file.zip

fpusan commented 5 months ago

The exit code -9 in the megahit code would suggest that you ran out of memory. A bit surprising since you have 128G RAM and not that many samples. Is this a workstation or a node within a computing cluster?

Manso002 commented 5 months ago

It is a workstation. The fasta files I'm working with occupy about 80gb, could that be an issue?

fpusan commented 5 months ago

If by this you mean the total size of the input fastq.gz files, then I suspect this may be indeed the problem. You may want to try using the sequential mode instead

Manso002 commented 5 months ago

I'll try that out and keep you updated. Thanks!