Weird signalp error

[Anto007]

Hi,

I'm testing out your new tool after having come across your interesting paper. I get the weird error Metascan needs signalp 3.0 or higher (see below for full log) for signalp despite having with me the signalp version 5.0b. Any help here would be appreciated.

(/home/username/tools/conda_samtools1.6_env) username@KW61042:~/tools/metascan$ ./metascan.pl test_data/
[16:25:11] Looking for 'barrnap' - found /home/username/tools/barrnap-0.6/bin/barrnap
[16:25:11] Determined barrnap version is 0.6
[16:25:11] Looking for 'blastn' - found /home/username/tools/ncbi-blast-2.12.0+/bin/blastn
[16:25:12] Determined blastn version is 2.12
[16:25:12] Looking for 'blastp' - found /home/username/tools/ncbi-blast-2.12.0+/bin/blastp
[16:25:13] Determined blastp version is 2.12
[16:25:13] Looking for 'bwa' - found /usr/bin/bwa
[16:25:13] Determined bwa version is 0.7
[16:25:13] Looking for 'egrep' - found /usr/bin/egrep
[16:25:13] Looking for 'find' - found /usr/bin/find
[16:25:13] Looking for 'grep' - found /usr/bin/grep
[16:25:13] Looking for 'hmmpress' - found /home/username/tools/hmmer-3.1b2/src/hmmpress
[16:25:13] Determined hmmpress version is 3.1
[16:25:13] Looking for 'hmmsearch' - found /home/username/tools/hmmer-3.1b2/src/hmmsearch
[16:25:13] Determined hmmsearch version is 3.1
[16:25:13] Looking for 'less' - found /usr/bin/less
[16:25:13] Looking for 'parallel' - found /usr/bin/parallel
[16:25:13] Determined parallel version is 20161222
[16:25:13] Looking for 'prodigal' - found /home/username/tools/prodigal
[16:25:13] Determined prodigal version is 2.6
[16:25:13] Looking for 'samtools' - found /home/username/tools/conda_samtools1.6_env/bin/samtools
[16:25:13] Determined samtools version is 1.6
[16:25:13] Looking for 'sed' - found /usr/bin/sed
[16:25:13] Looking for 'signalp' - found /usr/local/bin/signalp
Use of uninitialized value in concatenation (.) or string at ./metascan.pl line 254.
[16:25:14] Determined signalp version is 
Use of uninitialized value in numeric lt (<) at ./metascan.pl line 255.
[16:25:14] Metascan needs signalp 3.0 or higher. Please upgrade and try again.
(/home/username/tools/conda_samtools1.6_env) username@KW61042:~/tools/metascan$ which signalp
/usr/local/bin/signalp
(/home/username/tools/conda_samtools1.6_env) username@KW61042:~/tools/metascan$ /usr/local/bin/signalp --version
SignalP version 5.0b Linux x86_64

[Anto007]

I think the key to fixing this issue is line 255 but inserting my current version number instead of 4 breaks a lot of other tasks in the lines further below. Looks like I will need to spend a long time trying to debug this one and so I would appreciate if you've got any quick fixes in this regard.

if ($kingdom eq 'Bacteria' and $sigpver==3 || $sigpver==4) {

[gcremers]

Hi Anto,

Thanks for raising the issue.

I think the easiest way to get around the issue is to comment out lines 199 to 204 and not to use the --gram option. That should bypass the dependency check for signalp.

I will look for a better solution later.