Psiblast failed to retrieve sequences

Question

[Artisjoke]

I'm trying to obtain PSSMs for some 200 sequences, but was only able to obtain them for 29 sequences. My error log, however, is filled with hundreds upon hundreds of these warnings:

Warning: [psiblast] Failed to retrieve sequence gb|APO20772.1|
Warning: [psiblast] Failed to retrieve sequence gb|AFV99465.1|
Warning: [psiblast] Failed to retrieve sequence sp|D0VMR7.1|
Warning: [psiblast] Failed to retrieve sequence gb|ALS88442.1|
Warning: [psiblast] Failed to retrieve sequence gb|AMQ67166.1|
Warning: [psiblast] Failed to retrieve sequence ref|XP_024034203.1|
Warning: [psiblast] Failed to retrieve sequence ref|XP_015384778.2|
Warning: [psiblast] Failed to retrieve sequence gb|ATD14149.1|
Warning: [psiblast] Failed to retrieve sequence dbj|BBD88588.1|
Warning: [psiblast] Failed to retrieve sequence ref|XP_044490908.1|
Warning: [psiblast] Failed to retrieve sequence ref|XP_024033865.1|
Warning: [psiblast] Failed to retrieve sequence ref|XP_028063713.1|
Warning: [psiblast] Failed to retrieve sequence ref|XP_028111226.1|

This is an example of my command: psiblast -query A0RZI3.fasta -db nr -out pssm/A0RZI3.dat -num_iterations 2 -out_ascii_pssm pssm/A0RZI3.mat_ -num_threads 4

I tried googling the problem but came up empty. Does anyone have any ideas?

[lieven.sterck]

so it works for some of your queries but not for all ? (or do you also get those warnings for queries that do succeed? )

[Artisjoke]

Based on the error log, it's unclear whether I only get these warnings for the succeeding queries too, but I suspect I do.

[lieven.sterck]

Any way to check how the DB you use has been formatted?

[Artisjoke]

It's the non-redundant database from NCBI, I did check the md5 checksums which were fine. Is there anything else I should check in regards to the formatting?

[lieven.sterck]

did you download the pre-formatted one? otherwise I'm more thinking along the lines of which parameters have been used for formatting it.

Answer 1

[Artisjoke]

An update on my earlier question: what caused the problem is still unclear, but a new download of the databases solved the problem.