Commandline BLAST – errors?
I’m running command line blastx and blastp against a number of databases. However, running the exact same script on the exact same input files against the exact same databases occasionally seems to output different filesizes.
I can only assume that this is because the task is failing – but how can I QC the outputs to tell which output file was successful? I know I can look at the log files, but some of these I am inheriting and I want to be able to double check if they were successful.
The outputs tend to be outfmt6 or asn then converted to asn (I’m following a specific methodology, this isn’t my choice)
blastx -query /input-file.fa -db nr -num_threads 24 -max_target_seqs 10 -outfmt 11 -out output-file.asn blast_formatter -archive output-file.asn -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore" > output-file.outfmt6
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