Remote blast+ skipping query sequences

[arundurvasula]

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:

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.

Thanks!

[GenoMax]

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]

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

[seco]

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!