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.