I have been attempting to use command line blastp to search amino acid sequences from a transcriptome. I started with 34 sequences in the fasta, and got the error:
Error: CPU usage limit was exceeded, resulting in SIGXCPU (24)
So, I reduced the search fasta to 10 sequences, then to a single sequence. This is my current, complete fasta:
>lcl|TRINITY_DN16174_c0_g1_i1:47-397 ORF1_TRINITY_DN16174_c0_g1_i1:46:396
MRIHTGEKPYCCDICGKSFSVESTLTTHMRIHTGEKPYCCDICGKSFSGKNNLVHHRRTH
TGEKPYHCDVCGKSFIKSANLTIHKYSHTGEKPYHCDVCGKAFSQAGNLNTHKYVHT
I have used various iterations of the command trying to reduce the CPU load, including the two following:
blastp -db pdb -query high_priority_aa2.fasta -outfmt '6 qseqid score bitscore length pident stitle' -entrez_query "mollusca[ORGN]" -max_target_seqs 5 -max_hsps 1 -out high_priority_aa_blast_results2.txt -remote
and
blastp -db pdb -query high_priority_aa2.fasta -out high_priority_aa_blast_results2.txt -remote
I have tried the nr, swissprot and pdb databases. All iterations of commands and databases have resulted in the same error with the single sequence fasta.
Anyone have any ideas why this search is consuming so much CPU time on the remote server?