cannot execute hmmsearch when running spada.pl

[zhang iris]

Hi,

When I tried to run spada.pl, I got the error message showed below,

[16:22:36] #####  Stage 2 [Motif Mining]  #####

[16:22:36] cannot execute /home/ching/program/hmmer/hmmer-3.2.1//bin/hmmsearch

cannot execute /home/my_account/program/hmmer/hmmer-3.2.1//bin/hmmsearch at /home/my_account/program/spada_soft/spada/Hmm.pm line 432

This is the command line I used,

perl ~/program/spada_soft/spada/spada.pl --cfg ~/program/spada_soft/spada/cfg.txt --dir spada.crp.test --hmm ~/program/spada_soft/spada/hmm.crp/ --fas Athaliana_167_TAIR9.fa --gff Athaliana_167_TAIR10.gene_exons.gff3 --org Athaliana --sp --threads 2

I have set the hmm variable in the cfg.txt, and also tried:

1. `git pull` in the spada installed directory  

2. modify sqio.c in wise2.2.0/src/HMMer2 and `make all`

However, same error message pops out.

 

I have run hmmsearch in another project and it works well. So it might not because hmmer's installation errors.

Does anyone know how to fix it?

Any suggestions would be helpful.

[Chang Iris]

I have fixed the error, just revised the hmm variable setting in Hmm.pm and it works well.