Question: Command line argument error: Argument "query". File is not accessible: `psitmp24348007f0101.fasta'
0
gravatar for radha.jg
6 months ago by
radha.jg0
Uruguay
radha.jg0 wrote:

Hello all: I'm using psipred as follows:

runpsipred myfile.fasta

But it returns this error

Command line argument error: Argument "query". File is not accessible:  `psitmp24348007f0101.fasta'

Also I've downloded the uniprot files on the server and decompresed in multiple files:

ls uniref*
    uniref90.fasta         uniref90.fasta.08.phr  uniref90.fasta.16.pin  uniref90.fasta.24.psq  uniref90.fasta.33.phr
    uniref90.fasta.00.phr  uniref90.fasta.08.pin  uniref90.fasta.16.psq  uniref90.fasta.25.phr  uniref90.fasta.33.pin
    uniref90.fasta.00.pin  uniref90.fasta.08.psq  uniref90.fasta.17.phr  uniref90.fasta.25.pin  uniref90.fasta.33.psq ....

And it goes on and on, so why is this error happening and how do I run psipred properly?

Cheers

Jenifer

psipred sequence • 281 views
ADD COMMENTlink written 6 months ago by radha.jg0

Maybe you don t have write permission in the temporary dir?

ADD REPLYlink written 6 months ago by Asaf8.4k

Where does it save the temporary dir for me to check that?

ADD REPLYlink written 6 months ago by radha.jg0

I don't know, I would test if I have write permissions in the dir where I run the command first

ADD REPLYlink written 6 months ago by Asaf8.4k

No, the issue isn't the permissions, I have the right ones on the folder I'm running my stuff and the folder where the software was installed.

Anyway, I've tried a few things and triggered another error: it seems it doesn't find makemat (is supposedly included in the blast2 package installation, which I did), but it isn't there.

I'm about to quit this damn program to tell you the truth. At this point, any easier alternative will do

ADD REPLYlink written 6 months ago by radha.jg0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1299 users visited in the last hour