A trouble in using psiblast, blastdbcmd outputs empty file. why?

Question

[ygxing1]

Hi, every one!

I use psiblast to search the homologous protein sequences. Then use blastdbcmd to extract the exact homologous sequences based on the output file of psiblast. BUT I met a weird trouble as follows.

================ Below will get one seq output ===========

blastdbcmd -entry 99 -db ./db/test -dbtype prot -outfmt %f -out test.hits.fa

================= Below will get empty output ================

blastdbcmd -entry_batch fmt4 -db ./db/test -dbtype prot -outfmt %f -out test.hits.2.fa

======================================================

The file "fmt4" is like this :

===============================

PSIBLAST 2.7.1+
Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Stephen F.
Altschul, John C. Wootton, E. Michael Gertz, Richa Agarwala,
Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005)
"Protein database searches using compositionally adjusted
substitution matrices", FEBS J. 272:5101-5109.
Reference for composition-based statistics starting in round 2:
Alejandro A. Schaffer, L. Aravind, Thomas L. Madden, Sergei
Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and
Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST
protein database searches with composition-based statistics and
other refinements", Nucleic Acids Res. 29:2994-3005.

Database: db
           3 sequences; 498 total letters
Results from round 1
Query= T0658-D1
Length=166
                                                                      Score     E

Sequences producing significant alignments:                          (Bits)  Value
2  unnamed protein product                                            342     5e-127
1  unnamed protein product                                            342     5e-127
0  unnamed protein product                                            342     5e-127

Query_1 1 ADSIYVREQQIPILIDRIDNVLYEMRIPAQKGDVLNEITIQIGDNV  166

2     1   ADSIYVREQQIPILIDRIDNVLYEMRIPAQKGDVLNEITIQI  166

1     1   ADSIYVREQQIPILIDRIDNVLYEMRIPAQKGDVLNEITIQIGDNVDLSDI  166

0     1   ADSIYVREQQIPILIDRIDNVLYEMRIPAQKGDVLNEITIQI  166

Lambda      K        H        a         alpha
   0.316    0.133    0.379    0.792     4.96

=================================================

I am lost here. Could you give me some help? Great thanks in advance!

[GenoMax]

Does fmt4 file have one input entry gi/Accession # per line?

[ygxing1]

hi! Yes! there is. But I do not know how to post them clearly. Very sorry.

[GenoMax]

It looks like your fmt4 file has actual blast results. You can use only accession numbers (One per line) with -entry_batch directive.

[ygxing1]

Yes, this is a psiblast output file with "outfmt" equals 4. Do you know how to extract all the accession numbers from the output file?

There is a weird problem. I can extract the hits from some other fmt4 files. But I fail in some fmt4 files also.

comparing these fmt4 files carefully, I did not find any useful clues.

[GenoMax]

You should have used a tabular format for the results. It looks like this is a custom database of some sort, correct? It may be easier to re-run the blast otherwise you are going to need to parse this file.

[ygxing1]

Thank you very much! Yes, this is a custom database.

After one night enough sleep, I get your point.