Remote blast+ skipping query sequences

arundurvasula · 07-17-2014, 11:30 AM

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!

GenoMax · 07-17-2014, 04:07 PM

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/

maubp · 07-22-2014, 05:19 AM

Also report this as a bug to the NCBI Blast team.

seco · 08-20-2018, 01:27 PM

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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07-17-2014, 11:30 AM	#1
arundurvasula Member Location: California Join Date: Jun 2014 Posts: 16	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!

08-20-2018, 01:27 PM	#4
seco Junior Member Location: Egypt Join Date: Aug 2018 Posts: 2	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!

07-17-2014, 04:07 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	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/

07-22-2014, 05:19 AM	#3
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Also report this as a bug to the NCBI Blast team.