How many blast queries can be processed by remote blast calls with biopython’s Bio.Blast.NCBIWWW.qblast or BLAST+ with -remote flag? When I go above 1 sequence I get the following message near the top of my XML results file (and no results:
internal_error: (Severe Error) Blast search error: Details: search failed. # Informational Message: [blastsrv4.REAL]: Error: CPU usage limit was exceeded, resulting in SIGXCPU (24).
It seems strange for it to die on one protein sequence, so I may be doing something wrong. My reason for doing this is I thought it might be quicker to feed all my queries in one BLASTP call rather than one by one, but this may make no difference.
from Bio.Blast import NCBIXML
from Bio.Blast import NCBIWWW
from Bio import SeqIO
results_summaries = 
for query in SeqIO.parse(file_queries, format="fasta"):
result_handle = NCBIWWW.qblast("blastp", "nr", query.seq, expect = 1*(10**-6))
with open(f"filename.xml", "w") as out_handle:
with open(f"filename.xml",'r') as result_handle:
results = NCBIXML.read(result_handle)
max_bitscore = max([description.bits for description in results.descriptions])
top_hit = [description for description in results.descriptions if description.bits == max_bitscore]