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Old 07-17-2014, 11:30 AM   #1
Location: California

Join Date: Jun 2014
Posts: 16
Default Remote blast+ skipping query sequences


I'm running a remote blast on the nr database using some contigs I've assembled and I've noticed that it is skipping many contigs. Here's the command I'm using to search:

time blastx -db nr -query ../results/$sample/contigs/contig.fa -evalue 10 -matrix 'BLOSUM62' -word_size 3 -gapopen 11 -gapextend 1 -max_target_seqs 3 -outfmt "10 qseqid qlen sseqid evalue bitscore sskingdoms stitle sblastnames salltitles scomnames sscblyinames" -out ../results/$sample/blast/$sample-blast.csv -remote -seg "yes"
My terminal spits out a ton of errors like this:

Error: Error: internal_error: (Severe Error) Blast search error: Details: search failed. # Informational Message: [blastsrv4.REAL]: Error: CPU usage limit was exceeded, resulting in SIGXCPU (24).
which means that it's skipping a search because the CPU usage limit was exceeded. Is there anything I can do to make sure it doesn't skip these sequences? They are pretty important.

arundurvasula is offline   Reply With Quote
Old 07-17-2014, 04:07 PM   #2
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Location: East Coast USA

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You could split the file and then submit individual jobs via a shell script. Add some kind of delay between jobs to avoid overstepping the usage bounds.
GenoMax is offline   Reply With Quote
Old 07-22-2014, 05:19 AM   #3
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
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Also report this as a bug to the NCBI Blast team.
maubp is offline   Reply With Quote
Old 08-20-2018, 01:27 PM   #4
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Location: Egypt

Join Date: Aug 2018
Posts: 2

You can watch the currently running jobs and the stopped too using the jobs command
$ jobs -l
The -l is used to show the process ID.
Regarding the delay between the jobs, this tutorial explains Linux jobs and signals in detail.
Linux signals and jobs
Hope that helps!
seco is offline   Reply With Quote

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