Error: Could not find volume or alias file about cablastp HOT 9 CLOSED

It seems to be working fine over here:

[andrew@Serval cablastp] wget 'http://groups.csail.mit.edu/cb/cablastp/cablastp-nr20130630.tar.gz'
[andrew@Serval cablastp] tar xf cablastp-nr20130630.tar.gz
[andrew@Serval cablastp] l cablastp-nr20130630
total 20G
-rw-r--r-- 1 andrew users 417M Jul  8 14:57 blastdb-coarse.00.phr
-rw-r--r-- 1 andrew users  46M Jul  8 14:57 blastdb-coarse.00.pin
-rw-r--r-- 1 andrew users 954M Jul  8 14:57 blastdb-coarse.00.psq
-rw-r--r-- 1 andrew users 417M Jul  8 15:01 blastdb-coarse.01.phr
-rw-r--r-- 1 andrew users  46M Jul  8 15:01 blastdb-coarse.01.pin
-rw-r--r-- 1 andrew users 954M Jul  8 15:01 blastdb-coarse.01.psq
-rw-r--r-- 1 andrew users 466M Jul  8 15:05 blastdb-coarse.02.phr
-rw-r--r-- 1 andrew users  51M Jul  8 15:05 blastdb-coarse.02.pin
-rw-r--r-- 1 andrew users 954M Jul  8 15:05 blastdb-coarse.02.psq
-rw-r--r-- 1 andrew users 304M Jul  8 15:08 blastdb-coarse.03.phr
-rw-r--r-- 1 andrew users  33M Jul  8 15:08 blastdb-coarse.03.pin
-rw-r--r-- 1 andrew users 620M Jul  8 15:08 blastdb-coarse.03.psq
-rw-r--r-- 1 andrew users  245 Jul 12 02:01 blastdb-coarse.pal
-rw-r--r-- 1 andrew users 3.7G Jul  8 14:53 coarse.fasta
-rw-r--r-- 1 andrew users 175M Jul  8 14:53 coarse.fasta.index
-rw-r--r-- 1 andrew users 637M Jul  8 14:53 coarse.links
-rw-r--r-- 1 andrew users 175M Jul  8 14:53 coarse.links.index
-rw-r--r-- 1 andrew users    0 Jul  2 16:57 coarse.seeds
-rw-r--r-- 1 andrew users 9.7G Jul  8 14:45 compressed
-rw-r--r-- 1 andrew users 204M Jul  8 14:45 compressed.index
-rw-r--r-- 1 andrew users  272 Jul  8 14:45 params
[andrew@Serval cablastp] cablastp-search ./cablastp-nr20130630 ~/research/cablastp/data/test.fasta
Opening database in ./cablastp-nr20130630...
        Opening compressed database...
        Done opening compressed database.
        Opening coarse database...
        Done opening coarse database.
Done opening database in ./cablastp-nr20130630.

Blasting query on coarse database...
blastp -db cablastp-nr20130630/blastdb-coarse -num_threads 8 -outfmt 5 -dbsize 9281362451
Decompressing blast hits...
Blasting query on fine database...
blastp -subject /tmp/cablastp-fine-fasta397851578 -dbsize 9281362451 -num_threads 8
BLASTP 2.2.28+
[SNIPPED. RESULTS FOLLOW]

from cablastp.

Could you please:

1. Post precisely the command that you used. (You should do this for all future bug reports too!)
2. Post the results of ls -l on the compressed database directory.

from cablastp.

Here is the information you requested

1. Command used
   /path/cablastp-search --p="10" /nsarode3/blast_databases/cablastp_database/cablastp-nr20130630 /nsarode3/scratch/cablastp/stn1.fa --blast-args -max_target_seqs 10 -out stn1.blast -outfmt '6 qseqid sseqid pident qcovs length mismatch qstart qend sstart send evalue bitscore stitle'
2. Compressed database
   total 20G
   -rw-r--r-- 1 nsarode3 bio-stewart 272 Nov 5 17:41 params
   -rw-r--r-- 1 nsarode3 bio-stewart 204M Nov 5 19:14 compressed.index
   -rw-r--r-- 1 nsarode3 bio-stewart 9.7G Nov 5 17:17 compressed
   -rw-r--r-- 1 nsarode3 bio-stewart 0 Nov 5 19:29 coarse.seeds
   -rw-r--r-- 1 nsarode3 bio-stewart 175M Nov 5 19:15 coarse.links.index
   -rw-r--r-- 1 nsarode3 bio-stewart 637M Nov 5 19:07 coarse.links
   -rw-r--r-- 1 nsarode3 bio-stewart 175M Nov 5 19:18 coarse.fasta.index
   -rw-r--r-- 1 nsarode3 bio-stewart 3.7G Nov 5 19:02 coarse.fasta
   -rw-r--r-- 1 nsarode3 bio-stewart 245 Nov 5 19:07 blastdb-coarse.pal
   -rw-r--r-- 1 nsarode3 bio-stewart 620M Nov 5 19:23 blastdb-coarse.03.psq
   -rw-r--r-- 1 nsarode3 bio-stewart 33M Nov 5 19:09 blastdb-coarse.03.pin
   -rw-r--r-- 1 nsarode3 bio-stewart 304M Nov 5 19:17 blastdb-coarse.03.phr
   -rw-r--r-- 1 nsarode3 bio-stewart 954M Nov 5 19:29 blastdb-coarse.02.psq
   -rw-r--r-- 1 nsarode3 bio-stewart 51M Nov 5 19:32 blastdb-coarse.02.pin
   -rw-r--r-- 1 nsarode3 bio-stewart 466M Nov 5 19:31 blastdb-coarse.02.phr
   -rw-r--r-- 1 nsarode3 bio-stewart 954M Nov 5 17:41 blastdb-coarse.01.psq
   -rw-r--r-- 1 nsarode3 bio-stewart 46M Nov 5 19:08 blastdb-coarse.01.pin
   -rw-r--r-- 1 nsarode3 bio-stewart 417M Nov 5 17:25 blastdb-coarse.01.phr
   -rw-r--r-- 1 nsarode3 bio-stewart 954M Nov 5 13:00 blastdb-coarse.00.psq
   -rw-r--r-- 1 nsarode3 bio-stewart 46M Nov 5 19:08 blastdb-coarse.00.pin
   -rw-r--r-- 1 nsarode3 bio-stewart 417M Nov 5 19:12 blastdb-coarse.00.phr

from cablastp.

Odd. Could you cat /nsarode3/blast_databases/cablastp_database/cablastp-nr20130630/blastdb-coarse.pal and post the output here?

Your compressed database looks OK to me. There is something wrong wth blasting the regular blast database.

Could you also post the output of blastp -version?

Thanks!

from cablastp.

Here you go:

[nsarode3@biocluster-6 cablastp-nr20130630]$ cat /nsarode3/blast_databases/cablastp_database/cablastp-nr20130630/blastdb-coarse.pal 
#
# Alias file created: Jul 8, 2013  2:53 PM
#
TITLE cablastp-nr20130630/coarse.fasta
DBLIST cablastp-nr20130630/blastdb-coarse.00 cablastp-nr20130630/blastdb-coarse.01 cablastp-nr20130630/blastdb-coarse.02 cablastp-nr20130630/blastdb-coarse.03

Since I am running this on a cluster. I first load the ncbi blast module in my PBS script first. I have already finished using cablastp on one set of data, only it was against COG database that I compressed myself. So I doubt if the blast version could be an issue. In any case, here you go.

[nsarode3@biocluster-6 cablastp-nr20130630]$ module load ncbi_blast/2.2.28_binary 
[nsarode3@biocluster-6 cablastp-nr20130630]$ blastp -version
blastp: 2.2.28+
Package: blast 2.2.28, build Mar 12 2013 16:52:31

Thanks
Neha

from cablastp.

Shit. I just figured out the problem. Try cd /nsarode3/blast_databases/cablastp_database/ and then run cablastp-search.

I reproduced your problem by running cablastp-search from a different directory than the one that contains the blast database. Ug.

from cablastp.

I will do that. Our cluster is currently bogged down with jobs, so I can only let you know if this worked sometime tomorrow.

Neha

from cablastp.

Hopefully that will work for you. There is a fix in the pipeline, but in order to test it, I have to compress a sufficiently sized fasta file in order to get blast to create the alias file.

In the mean time, you can either:

1. Run cablastp-search in the directory that contains the compressed database
2. Hand edit the blastdb-coarse.pal alias file inside the compressed database so that all instances of cablastp-nr20130630/X are changed to just X. Then you should be able to run cablastp-search from any directory.

from cablastp.

I think this should be fixed in commit 9864e98.

from cablastp.