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Error: CPU usage limit was exceeded, resulting in SIGXCPU (24) on remote blastp search

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?

blast
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updated by GenoMax GenoMax • written by klo • klo

1 answer

While this is not going to help answer why you got that error, I was able to run your query in under 3-4 min without an error against follwing. I would say try again.

With PDB

$ more high_priority_aa_blast_results2.txt 
lcl|TRINITY_DN16174_c0_g1_i1:47-397     40      20.0    26      30.769  Crystal structure of octopus S-crystallin Q108F mutant in complex with glutathione [Oc
topus vulgaris]

With Swissprot

$ more high_priority_aa_blast_results2.txt 
lcl|TRINITY_DN16174_c0_g1_i1:47-397     71      32.0    47      38.298  RecName: Full=Protein hunchback [Bithynia tentaculata]
lcl|TRINITY_DN16174_c0_g1_i1:47-397     67      30.4    43      39.535  RecName: Full=Protein hunchback [Bithynia tentaculata]
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written by GenoMax GenoMax

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