Remote blast+ skipping query sequences

Question

[biobio]

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!

[Devon Ryan]

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

[biobio]

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?

[Devon Ryan]

It's worth a try.

[pld]

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.

[6schulte]

I have the same problem today... You haven't happened to have found the solution, did you? I'd be grateful! Thx

[MCA]

Hi! I am also having this problem, I am doing a remote blastp using entrez_query to limit by organism, sending 50 queries in an imput file, and taking only the first 5 matches. did you find a solution?