Issue with formatting NR database with mpiformatdb

Question

[abhijeetpnwr]

I have been using mpiBlast for some time. I am trying to format latest NR database with mpiformatdb but it gives following errors:

Sequence id "" is not parseable. Formating failed at

ERROR: [000.000] FDBDumpDeflineAsn() failed. Formating terminated abnormaly

Removed single-volume database ./nr.015

FATAL ERROR: [001.000] Fatal error when adding sequence to BLAST database.

Command I have used for formatting is : mpiformatdb -N 16 -i ./nr -o T -p T

When I try mpiformatdb with some other smaller databases and sequence files , It works fine and formats properly.

[karimy]

Hi, Have you found a solution to this problem? I am facing the same issue as a part of my research. Kindly let me know if you figure it out and I'll let you know too.

Thanks

Answer 1

[goughes]

I ran into this problem as well. The solution is to remove the ctrl-A (^A) characters that are present in the comment lines. Here is a way to do it with sed. There are a few others as well, outlined here: https://stackoverflow.com/questions/15421478/how-to-remove-ctrl-a-characters-from-file-using-sed

sed -i -e 's/\x01//g' est_mouse