Question: Remote blast+ skipping query sequences
gravatar for biobio
6.0 years ago by
United States
biobio40 wrote:



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.



blast blastx • 2.9k views
ADD COMMENTlink modified 5.9 years ago by Biostar ♦♦ 20 • written 6.0 years ago by biobio40

What's the output of ulimit -a? I'm guessing that there's a CPU time limit on the server.

ADD REPLYlink written 6.0 years ago by Devon Ryan95k

Well this is a remote query so it's on NCBI's servers so I don't think I can send them that command. However, I believe you are right. Would it be possible to split up my longer sequences to shorten the amount of time it's searching?

ADD REPLYlink written 6.0 years ago by biobio40

It's worth a try.

ADD REPLYlink written 6.0 years ago by Devon Ryan95k

I know with Entrez there is a limit to the number of queries you can submit per second, you may want to alter the way you're sending the blast jobs to reduce the number of jobs you're submitting at once.

ADD REPLYlink written 6.0 years ago by pld4.8k
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