error in addss.pl

[acpguedes]

Hi,

I'm getting this error to any alignment I try to add 2nd structure.

(base) acpguedes@haldane:~/projects/sig_trans/work/SBP_5/20190730/test2/hhsuite_teste_SBP$ addss.pl aln_base/WP_009507761.1..90-379.aln t.exp -fas
$ /home/linuxbrew/anaconda3/scripts/reformat.pl -v 1 -M first fas a3m aln_base/WP_009507761.1..90-379.aln /tmp/YmzgFUOmbl/tyXTA1Jw6N.in.a3m
$ hhconsensus -i /tmp/YmzgFUOmbl/tyXTA1Jw6N.in.a3m -s /tmp/YmzgFUOmbl/tyXTA1Jw6N.sq -o /tmp/YmzgFUOmbl/tyXTA1Jw6N.in.a3m > /dev/null
- 14:56:20.394 INFO: /tmp/YmzgFUOmbl/tyXTA1Jw6N.in.a3m is in A2M, A3M or FASTA format

Filtering alignment to diversity 7 ...
$ hhfilter -v 1 -neff 7 -i /tmp/YmzgFUOmbl/tyXTA1Jw6N.in.a3m -o /tmp/YmzgFUOmbl/tyXTA1Jw6N.in.a3m
$ /home/linuxbrew/anaconda3/scripts/reformat.pl -v 1 -r -noss a3m psi /tmp/YmzgFUOmbl/tyXTA1Jw6N.in.a3m /tmp/YmzgFUOmbl/tyXTA1Jw6N.in.psi
Predicting secondary structure with PSIPRED ... $ /cluster/toolkit/production/bioprogs/blast/bin/blastpgp -b 1 -j 1 -h 0.001 -d /home/linuxbrew/anaconda3/data/do_not_delete -i /tmp/YmzgFUOmbl/tyXTA1Jw6N.sq -B /tmp/YmzgFUOmbl/tyXTA1Jw6N.in.psi -C /tmp/YmzgFUOmbl/tyXTA1Jw6N.chk 1> /tmp/YmzgFUOmbl/tyXTA1Jw6N.blalog 2> /tmp/YmzgFUOmbl/tyXTA1Jw6N.blalog

Error: command '/cluster/toolkit/production/bioprogs/blast/bin/blastpgp -b 1 -j 1 -h 0.001 -d /home/linuxbrew/anaconda3/data/do_not_delete -i /tmp/YmzgFUOmbl/tyXTA1Jw6N.sq -B /tmp/YmzgFUOmbl/tyXTA1Jw6N.in.psi -C /tmp/YmzgFUOmbl/tyXTA1Jw6N.chk 1> /tmp/YmzgFUOmbl/tyXTA1Jw6N.blalog 2> /tmp/YmzgFUOmbl/tyXTA1Jw6N.blalog' returned error code 127

$ echo tyXTA1Jw6N.chk > /tmp/YmzgFUOmbl/tyXTA1Jw6N.pn

$ echo tyXTA1Jw6N.sq  > /tmp/YmzgFUOmbl/tyXTA1Jw6N.sn

$ /cluster/toolkit/production/bioprogs/blast/bin/makemat -P /tmp/YmzgFUOmbl/tyXTA1Jw6N

Error: failed to execute '/cluster/toolkit/production/bioprogs/blast/bin/makemat -P /tmp/YmzgFUOmbl/tyXTA1Jw6N': No such file or directory

I think it is related to how my server are organized:

(base) acpguedes@haldane:~/projects/sig_trans/work/SBP_5/20190730/test2/hhsuite_teste_SBP$ which makemat 
/home/linuxbrew/.linuxbrew/bin/makemat
(base) acpguedes@haldane:~/projects/sig_trans/work/SBP_5/20190730/test2/hhsuite_teste_SBP$ which blastpgp 
/home/linuxbrew/.linuxbrew/bin/blastpgp

But, looking to the script to try to fix it but I didn't find how the variable $ncbidir is defined.

I'd like a hint to how make it work.

Thanks in advance.

[milot-mirdita]

The scripts folder where addss.pl resides also has a HHPaths.pm file which contains all the paths to the software packages/databases. You need to setup legacy blast, current BLAST+ does not work the addss.pl.

That part is a huge mess and we don't have the resources/funding to improve the situation :/