Help For Blastx, No Output Untill The Program Finished

Question

[zhangmin8712]

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

Answer 1

[Istvan Albert]

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.

[Lee Katz]

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.

[Michael]

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.