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Help For Blastx, No Output Untill The Program Finished

I have run blastx program agaist NR with about 50,000 sequences locally. I am confused the xml file is empty, but the blastx program is still running. However, I have tried with 22 sequences, it's OK. I wander if the blastx program print results untill the program finished. Thanks, my commond is

blastx -query hybrid.cd-hit.filter.fasta -db nr-out assembly.blast_nr.xml -evalue 1e-5 -outfmt 5 -max_target_seqs 1 -num_threads 10
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updated by Istvan Albert Istvan Albert • written by zhangmin8712 • zhangmin8712

1 answer

The output of most programs is buffered at the operating system level. This means that the output is produced in spurts, when the buffer fills up or when the program terminates.

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written by Istvan Albert Istvan Albert

This is correct. A way of getting output more quickly would be to run the command once per query, but it would slow BLAST significantly.

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written by Lee Katz Lee Katz

Another way could be to use standard format, or tabular format, when I last checked the output appeared more or less in a constant stream while the sequences were processed. Maybe this is different for the XML writer.

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written by Michael Dondrup Michael Dondrup

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