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bjornwallner / ProQ_scripts

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bug : runing run_test.sh #1

Open fatraore opened 6 years ago

fatraore commented 6 years ago

Hello, I tried to run the run_test.sh script but i have this error message: 

[blastpgp] WARNING: Unable to open uniref90.pin
Running Makemat...
[makemat] FATAL ERROR: Unable to open file psitmp.29354.chk.

I had this message too but I've already installed emboss:

Assuming file is a pdb
readline() on closed filehandle FILE at /home/netbook/Documents/ProjetLong/proqM/ProQ_scripts/bin/profile_subset.pl line 26.
needle from the EMBOSS package needs to be installed.
readline() on closed filehandle FILE at /home/netbook/Documents/ProjetLong/proqM/ProQ_scripts/bin/profile_subset.pl line 26.
needle from the EMBOSS package needs to be installed.
readline() on closed filehandle FILE at /home/netbook/Documents/ProjetLong/proqM/ProQ_scripts/bin/ss2_subset.pl line 69.
readline() on closed filehandle FILE at /home/netbook/Documents/ProjetLong/proqM/ProQ_scripts/bin/ss2_subset.pl line 89.
needle from the EMBOSS package needs to be installed.

Have you an idea about that?

Thank you

bjornwallner commented 6 years ago

Do you have a formatted uniref90 database? The first error says it cannot find the database.

fatraore commented 6 years ago

I did not have it but I downloaded it and put it in the bin directory ( and set the path in bin/run_all_external.pl ), but I got the same error message

Kaixiang-Wang commented 2 years ago

Has BUG "needle from the EMBOSS package needs to be installed" been solved? and how?

Thank you!