diamond (blastp) exit codes

sapuizait

New member
Does anyone know where I can find what the exit codes mean? is there a list or a website? Trying to run a $diamond blastp (on a server) and I am getting an exit code -6 and I have no idea what this means. I also looked around and I cant find anything.

Cheers,
P
 

sapuizait

New member
hey,
thanks for your quick reply, so here is some background info:
I am using diamond blastp in order to perform binning of assembled contigs of a metagenome. As reference I am using the nr database. The whole process is part of a pipeline called autometa and does metagenomic binning.

Here is the last few lines of the logfile:


"make_taxonomy_table.py, run_command: diamond blastp --query filtered.orfs.faa --db /databases/nr.dmnd --evalue 1e-5 --max-target-seqs 200 -p 32 --outfmt 6 --out filtered.orfs.blastp -t /tmp
Error when performing diamond blastp:
-6
Attempting to correct by rebuilding nr...

building nr.dmnd database, this may take some time
make_taxonomy_table.py, run_command: diamond blastp --query filtered.orfs.faa --db /databases/nr.dmnd --evalue 1e-5 --max-target-seqs 200 -p 32 --outfmt 6 --out filtered.orfs.blastp -t /tmp
make_taxonomy_table.py: Error, the command:
diamond blastp --query filtered.orfs.faa --db /databases/nr.dmnd --evalue 1e-5 --max-target-seqs 200 -p 32 --outfmt 6 --out filtered.orfs.blastp -t /tmp
failed, with exit code -6
Stop job: mar. mars 24 15:06:01 CET 2020"
 

sapuizait

New member
Cannot get a hold of the administrator. I ran it one more time and asked for an error file which gave me the following:
"Start job:jeu. mars 26 11:38:59 CET 2020
No such file or directory
Error: Error calling stat on file /storage/databanks/bio/autometa/databases/nr.gz
Stop job: jeu. mars 26 17:31:38 CET 2020"

Could be that the nr.gz file is missing?
If I hear back from the admin of the server, will post an update
 

Benjamin Buchfink

Administrator
Staff member
Yes, this error means that the file does not exist. It could be that you can't access this file from a compute node on your cluster, while you can from the login node.
 
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