panaroo-qc error 24: too many open files

[gtonkinhill]

panaroo-qc error 24: too many open files

[tseemann]

your system limits files per process:

ulimit -n  
102400

often it is 4096 which is too small.
you can try increasing with ulimit -n 16384 etc
but ultimately you will need sysadmin to alter /etc/limits.conf or similar.

[svanhal71]

Thanks that sorted the problem however I now get
ERROR: could not open "refseq.genomes.k21.s1000.msh" for reading (downloaded from https://mash.readthedocs.io/en/latest/tutorials.html).
Suggestions?
Thx

[gtonkinhill]

This looks like you might have a problem with the path to "refseq.genomes.k21.s1000.msh". Can you double check the file exists and is readable? You could try running "head" on the file.

[svanhal71]

The file is readable and have moved it to the same folder as the data - same error.

Thx

[tseemann]

What do these say:

realpath refseq.genomes.k21.s1000.msh
ls -lsa refseq.genomes.k21.s1000.msh

[svanhal71]

Thanks
Got it to work now.