Sock::connect error with blast_formatter 2.2.28+

[meetasunil]

Hello,
I've been getting the following error with the latest as well as older versions of blast+, specifically with the blast_formatter command:

Error: (311.22) SOCK#1000[?]: [SOCK::Connect] Failed SOCK_gethostbyname("www.ncbi.nlm.nih.gov")
Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:80: Unknown

I'm just using the standalone version and do not understand the need for blast_formatter to try to connect to the ncbi server. The command-line that I use with blast_formatter is as exemplified below:

blast_formatter -archive file.ASN.1 -outfmt 0 -out file.aln

It has worked properly before but one fine day I start getting this error..
Can anyone please help? It's a little urgent for me.


Thanks and regards,
Meeta
India

[cjfields]

I had the same problem using a local database. The problem appears to be that blast_formatter looks for the database locally first using the path given for the database in the BLAST run; if it isn't found, then it tries remotely (and of course won't find it if there is no network or the DB is custom).

In my situation, I had given it a relative path with output redirected to a different folder, so when I attempted to use blast_formatter from that folder, the database couldn't be found using the relative path. I simply moved the data back to where I ran the initial BLAST calls (relative path matched the database location) and got it working. The immediate solution to avoid this altogether is to always use an absolute path when running local BLAST.

Hello,
I've been getting the following error with the latest as well as older versions of blast+, specifically with the blast_formatter command:

Error: (311.22) SOCK#1000[?]: [SOCK::Connect] Failed SOCK_gethostbyname("www.ncbi.nlm.nih.gov")
Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:80: Unknown

I'm just using the standalone version and do not understand the need for blast_formatter to try to connect to the ncbi server. The command-line that I use with blast_formatter is as exemplified below:

blast_formatter -archive file.ASN.1 -outfmt 0 -out file.aln

It has worked properly before but one fine day I start getting this error..
Can anyone please help? It's a little urgent for me.


Thanks and regards,
Meeta
India