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

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

Hi,

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:

Code:
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:

Code:
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.

Thanks!
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Old 07-17-2014, 04:07 PM   #2
GenoMax
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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. http://www.cyberciti.biz/faq/linux-u...ash-scripting/
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Old 07-22-2014, 05:19 AM   #3
maubp
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Also report this as a bug to the NCBI Blast team.
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Old 08-20-2018, 01:27 PM   #4
seco
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Location: Egypt

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You can watch the currently running jobs and the stopped too using the jobs command
Code:
$ 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!
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