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morgannprice / PaperBLAST

PaperBLAST: find papers about a protein or its homologs
http://papers.genomics.lbl.gov
GNU General Public License v3.0
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Issues with local GapMind installation #11

Closed mgabriell1 closed 8 months ago

mgabriell1 commented 8 months ago

Hi, I'm trying to install GapMind locally to be able to analyze multiple genomes at once. I've followed the instructions in SETUP, but I'm having some issues regarding performing the analysis. In fact, when I run gapsearch.pl I get the following error:

hmmsearch failed to create /tmp/gapsearch.74181.PF01502.domtbl
<h1>Software error:</h1>
<pre>Command failed
../bin/gapsearch.pl -orgs ../tmp/NCBI__GCF_902167245.1/orgs -set aa -out ../tmp/NCBI__GCF_902167245.1/aa.hits -nCPU 12

Given that the error seems to arise due to the fact that there are no write permission to tmp I changed the tmp folder in the source code to ../tmp in lines 150 and 184 (edits below). 

L150:    my $tmpfile = "../tmp/gapsearch.$$.$hmmId.domtbl";
L184:    my $cfile = "..//tmp/gapsearch.$$.curated";

Now I have another error though regarding line 156. The output of gapsearch.pl is gere:

bin/gapsearch.pl -orgs tmp/NCBI__GCF_902167245.1/orgs -set aa -out tmp/NCBI__GCF_902167245.1/aa.hits 
Comparing 1 proteomes to 145 HMMs and 6284 sequences
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpectedSyntax error: "(" unexpected

cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
All 145 HMM analyses complete
hmmsearch failed to create ../tmp/gapsearch.75445.PF01502.domtbl

How can I solve this issue? Thanks for the support.

Marco

morgannprice commented 8 months ago

I haven't seen this error before. It looks like there's something wrong with the hmm files that hmmsearch is trying to read. You can run gapsearch.pl with -verbose to see exactly how it is invoking hmmsearch.

Also, did you run

bin/extractHmms.pl tmp/path.aa/steps.db tmp/path.aa

If yes, please check that the hmms files in tmp/path.aa look ok, i.e. the first few lines of PF00380.19.hmm should be HMMER3/f [3.1b2 | February 2015] NAME Ribosomal_S9 ACC PF00380.19 DESC Ribosomal protein S9/S16

and it should end with the line //

-- Morgan

mgabriell1 commented 8 months ago

Hi, Thanks for the quick reply. I ran extractHmms.pl (it extracted around 145 HMMs, if I remember correctly). The one that you specified is not present in tmp/path.aa , but other than that all the other requirements are met.

This is the verbose output of gapsearch:

$ bin/gapsearch.pl -orgs tmp/NCBI__GCF_902167245.1/orgs -set aa -out tmp/NCBI__GCF_902167245.1/aa.hits -verbose
Comparing 1 proteomes to 145 HMMs and 6284 sequences
Running PF01502
Running PF01817
Running PF02965
Waiting
Running PF14574
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00007
Waiting
Running TIGR00032
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR00033
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Done waiting
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR00034
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00036
Waiting
Done waiting
Running TIGR00069
Waiting
Done waiting
Running TIGR00070
Waiting
Running TIGR00110
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00112
Done waiting
Waiting
Done waiting
Running TIGR00118
Waiting
Running TIGR00119
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Waiting
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Running TIGR00132
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00133
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Done waiting
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Done waiting
Running TIGR00134
Waiting
Running TIGR00135
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00169
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00170
Done waiting
Waiting
Running TIGR00171
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Running TIGR00191
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR00260
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00262
Waiting
Running TIGR00263
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR00338
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00407
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00419
Waiting
Running TIGR00458
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00465
Done waiting
Waiting
Running TIGR00470
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00507
Waiting
Done waiting
Running TIGR00564
Waiting
Running TIGR00565
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00566
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00652
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Waiting
Running TIGR00653
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00656
Waiting
Running TIGR00657
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00658
Done waiting
Waiting
Running TIGR00669
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00674
Waiting
Running TIGR00735
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00761
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR00838
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00938
Waiting
Running TIGR00965
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00970
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Done waiting
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR00973
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00977
Waiting
Running TIGR00978
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01001
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01027
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR01048
Done waiting
Waiting
Running TIGR01088
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01093
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01122
Waiting
Running TIGR01123
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01124
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01127
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01136
Done waiting
Waiting
Running TIGR01137
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR01138
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01139
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01141
Done waiting
Waiting
Running TIGR01172
Done waiting
Waiting
Running TIGR01245
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01246
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01251
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01261
Waiting
Running TIGR01264
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01267
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01268
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Waiting
Done waiting
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Running TIGR01296
Waiting
Running TIGR01327
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01346
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01356
Waiting
Done waiting
Running TIGR01357
Waiting
Running TIGR01358
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01361
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01364
Waiting
Done waiting
Running TIGR01365
Waiting
Running TIGR01366
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01368
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01369
Done waiting
Waiting
Running TIGR01371
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR01392
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01520
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01521
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01536
Waiting
Running TIGR01745
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01791
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01795
Done waiting
Waiting
Done waiting
Running TIGR01796
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Waiting
Running TIGR01797
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01799
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01801
Waiting
Done waiting
Running TIGR01802
Waiting
Running TIGR01805
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01806
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01807
Waiting
Running TIGR01808
Done waiting
Waiting
Running TIGR01809
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01815
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01820
Waiting
Running TIGR01850
Done waiting
Waiting
Running TIGR01851
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01855
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01859
Waiting
Done waiting
Running TIGR01885
Waiting
Running TIGR01890
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01892
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01900
Waiting
Done waiting
Running TIGR01920
Waiting
Running TIGR01921
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02067
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02078
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02079
Done waiting
Waiting
Running TIGR02080
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Waiting
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Running TIGR02082
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02083
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR02084
Waiting
Running TIGR02086
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR02087
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02129
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR02130
Waiting
Done waiting
Running TIGR02137
Waiting
Running TIGR02146
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02153
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02316
Done waiting
Waiting
Running TIGR02539
Done waiting
Waiting
Running TIGR02660
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR03105
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR03188
Waiting
Done waiting
Running TIGR03246
Waiting
Running TIGR03455
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR03532
Done waiting
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
Waiting
Done waiting
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Running TIGR03535
Waiting
Done waiting
Running TIGR03536
Waiting
Running TIGR03537
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR03538
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR03539
Waiting
Done waiting
Running TIGR03540
Running TIGR03542
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST/bin/hmmsearch: 1: Syntax error: "(" unexpected
cmd failed: No such file or directory at bin/gapsearch.pl line 156.
All 145 HMM analyses complete
hmmsearch failed to create ../tmp/gapsearch.18966.PF01502.domtbl
morgannprice commented 8 months ago

The syntax error from hmmsearch suggests that the *.hmm files are not correct. Please check the tmp/path.aa/TIGR03542.hmm file, it should start with these lines:

HMMER3/f [3.1b2 | February 2015] NAME TIGR03542 ACC TIGR03542 DESC DAPAT_plant: LL-diaminopimelate aminotransferase LENG 402

Also, I pushed an update to gapsearch.pl to report the actual command that failed, which might help make it clearer what is going on.

mgabriell1 commented 7 months ago

Hi, Sorry for the wait. The HMM files seem to be correct (example below) and I have 145 of them (I don't know if this is the correct number).

HMMER3/f [3.1b2 | February 2015]
NAME  TIGR03542
ACC   TIGR03542
DESC  DAPAT_plant: LL-diaminopimelate aminotransferase
LENG  402
ALPH  amino
...
\\

After getting the updated gapsearch version the error changed to what you find below. The tmp/NCBI__GCF_902167245.1/orgs.faa exists as well as the Syntax error: "(" unexpected error. What could be the cause? Thanks for the help!

$ bin/gapsearch.pl -orgs tmp/NCBI__GCF_902167245.1/orgs -set aa -out tmp/NCBI__GCF_902167245.1/aa.hits -verbose
Comparing 1 proteomes to 145 HMMs and 6284 sequences
Running PF01502
Running PF01817
Running PF02965
Waiting
Running PF14574
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.PF01817.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/PF01817.21.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.PF01502.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/PF01502.18.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.PF02965.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/PF02965.17.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.PF14574.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/PF14574.6.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00007
Done waiting
Waiting
Running TIGR00032
Done waiting
Waiting
Done waiting
Running TIGR00033
Waiting
Running TIGR00034
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00007.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00007.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00032.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00032.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00033.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00033.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00034.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00034.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00036
Done waiting
Waiting
Running TIGR00069
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00036.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00036.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Done waiting
Running TIGR00070
Waiting
Running TIGR00110
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00070.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00070.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00110.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00110.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00069.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00069.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00112
Waiting
Done waiting
Running TIGR00118
Waiting
Running TIGR00119
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00112.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00112.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00118.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00118.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00119.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00119.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR00132
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00132.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00132.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00133
Done waiting
Waiting
Done waiting
Running TIGR00134
Waiting
Done waiting
Running TIGR00135
Waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
Running TIGR00169
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00133.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00133.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00134.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00134.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00169.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00169.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00135.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00135.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00170
Waiting
Running TIGR00171
Done waiting
Waiting
Done waiting
Running TIGR00191
Waiting
Running TIGR00260
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00170.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00170.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00171.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00171.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00191.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00191.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00260.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00260.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Running TIGR00262
Waiting
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00262.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00262.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Done waiting
Running TIGR00263
Waiting
Done waiting
Running TIGR00338
Waiting
Running TIGR00407
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpectedSyntax error: "(" unexpected

/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00263.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00263.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00407.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00407.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00338.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00338.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00419
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00419.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00419.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR00458
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00458.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00458.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00465
Waiting
Running TIGR00470
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00465.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00465.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00470.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00470.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00507
Waiting
Running TIGR00564
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00507.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00507.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00564.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00564.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00565
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
Waiting
Running TIGR00566
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00565.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00565.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00566.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00566.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR00652
Done waiting
Waiting
Running TIGR00653
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00652.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00652.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00653.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00653.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Done waiting
Running TIGR00656
Waiting
Running TIGR00657
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00656.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00656.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00657.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00657.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00658
Waiting
Running TIGR00669
Done waiting
Waiting
Done waiting
Running TIGR00674
Waiting
Running TIGR00735
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00669.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00669.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00658.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00658.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00674.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00674.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00735.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00735.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00761
Waiting
Done waiting
Running TIGR00838
Waiting
Done waiting
Running TIGR00938
Waiting
Running TIGR00965
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00761.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00761.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00838.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00838.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00938.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00938.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00965.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00965.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR00970
Waiting
Done waiting
Running TIGR00973
Waiting
Done waiting
Running TIGR00977
Waiting
Running TIGR00978
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00970.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00970.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00973.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00973.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00977.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00977.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR00978.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR00978.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01001
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01001.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01001.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01027
Waiting
Done waiting
Running TIGR01048
Waiting
Running TIGR01088
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpectedSyntax error: "(" unexpected

/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01048.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01048.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01027.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01027.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01088.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01088.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01093
Waiting
Done waiting
Running TIGR01122
Waiting
Running TIGR01123
Done waiting
Waiting
Running TIGR01124
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01093.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01093.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01122.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01122.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01123.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01123.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01124.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01124.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01127
Done waiting
Waiting
Done waiting
Running TIGR01136
Waiting
Done waiting
Running TIGR01137
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01127.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01127.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR01138
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01136.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01136.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01137.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01137.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01138.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01138.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01139
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01139.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01139.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01141
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01141.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01141.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01172
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
Waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01172.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01172.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Running TIGR01245
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01245.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01245.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01246
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01246.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01246.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01251
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01251.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01251.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01261
Waiting
Running TIGR01264
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01261.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01261.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01264.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01264.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01267
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01267.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01267.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01268
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01268.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01268.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Done waiting
Running TIGR01296
Waiting
Running TIGR01327
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01296.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01296.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01327.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01327.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01346
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01346.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01346.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01356
Waiting
Done waiting
Running TIGR01357
Waiting
Running TIGR01358
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpectedSyntax error: "(" unexpected

/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01358.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01358.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01357.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01357.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01356.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01356.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01361
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01361.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01361.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01364
Waiting
Running TIGR01365
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
Waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01364.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01364.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
Running TIGR01366
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01365.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01365.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01366.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01366.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01368
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01368.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01368.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01369
Waiting
Done waiting
Running TIGR01371
Waiting
Running TIGR01392
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01369.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01369.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01371.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01371.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01392.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01392.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01520
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01520.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01520.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01521
Waiting
Done waiting
Running TIGR01536
Waiting
Running TIGR01745
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01521.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01521.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01536.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01536.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01745.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01745.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01791
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01791.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01791.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01795
Waiting
Running TIGR01796
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01795.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01795.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Done waiting
Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01796.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01796.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR01797
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01797.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01797.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01799
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01799.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01799.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01801
Waiting
Done waiting
Running TIGR01802
Waiting
Running TIGR01805
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01801.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01801.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01802.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01802.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01805.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01805.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01806
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01806.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01806.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR01807
Waiting
Done waiting
Running TIGR01808
Waiting
Running TIGR01809
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpectedSyntax error: "(" unexpected

/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01808.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01808.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01807.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01807.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01809.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01809.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01815
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01815.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01815.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01820
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01820.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01820.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01850
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01850.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01850.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR01851
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01851.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01851.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01855
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01855.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01855.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01859
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01859.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01859.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01885
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01885.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01885.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01890
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01890.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01890.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01892
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01892.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01892.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01900
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01900.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01900.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01920
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01920.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01920.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR01921
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR01921.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR01921.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02067
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02067.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02067.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02078
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02078.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02078.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR02079
Waiting
Running TIGR02080
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02079.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02079.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02080.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02080.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02082
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02082.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02082.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02083
Done waiting
Waiting
Running TIGR02084
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02083.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02083.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02084.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02084.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02086
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02086.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02086.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02087
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02087.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02087.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02129
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02129.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02129.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR02130
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02130.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02130.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02137
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02137.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02137.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02146
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02146.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02146.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02153
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02153.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02153.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR02316
Waiting
Running TIGR02539
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02316.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02316.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02539.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02539.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR02660
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR02660.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR02660.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR03105
Waiting
Running TIGR03188
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: /home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR03188.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR03188.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR03105.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR03105.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR03246
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR03246.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR03246.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR03455
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR03455.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR03455.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Done waiting
Running TIGR03532
Waiting
Running TIGR03535
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR03532.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR03532.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR03535.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR03535.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Running TIGR03536
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR03536.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR03536.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR03537
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR03537.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR03537.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Waiting
Running TIGR03538
Done waiting
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR03538.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR03538.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Waiting
Done waiting
Running TIGR03539
Waiting
Running TIGR03540
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR03539.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR03539.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR03540.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR03540.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
Done waiting
Running TIGR03542
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch: 1: Syntax error: "(" unexpected
/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.TIGR03542.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/TIGR03542.hmm tmp/NCBI__GCF_902167245.1/orgs.faa failed: No such file or directory at bin/gapsearch.pl line 156.
All 145 HMM analyses complete
hmmsearch failed to create /tmp/gapsearch.25813.PF01502.domtbl
morgannprice commented 7 months ago

Maybe something is wrong with your hmmsearch executable? Or maybe your /tmp directory isn't writable ?

What happens if you run one of the hmmsearch commands by itself, i.e.

/home/marco/GapMind/PaperBLAST-master/bin/hmmsearch --cut_tc -o /dev/null --domtblout /tmp/gapsearch.25813.PF01817.domtbl /home/marco/GapMind/PaperBLAST-master/bin/../tmp/path.aa/PF01817.21.hmm tmp/NCBI__GCF_902167245.1/orgs.faa

-- Morgan

mgabriell1 commented 7 months ago

Ok, I've figured out the error. Based on the instruction in SETUP I understood that I needed to only put in bin the hmmsearch and hmmfetch files as found in the indicated archive under src/ (which now I realize that is not the case). Installing hmmer locally and setting a soft link from those executable to the required GapMind files solved this issue. Maybe it could be worth to explain this passage better in the software documentation. In any case, thanks for the help!

Marco