Signal P Compatibility Error?

[andypaige772]

Hello,

I am trying to install and use signalP. Which version of signalP works with TransPi?

I tried installing v6 and v5. I get similar errors as below , so we changed the nextflow.config file from "-f short -n 4.signalp.out 4.combined.okay.fa.transdecoder.pep" to be "-format short -stdout 2.signalp.out -fasta 2.combined.okay.fa.transdecoder.pep" and are still getting error messages. Is this because we are using an incompatible version or is there a different error you could help us fix? Thank you for your help.

Error executing process > 'signalP_trinotate (4)'

Caused by:
Process signalP_trinotate (4) terminated with an error exit status (2)

Command executed:

#signalP to predict signal peptides

echo -e "\n-- Starting with SignalP --\n"

/usr/local/bin/signalp -f short -n 4.signalp.out 4.combined.okay.fa.transdecoder.pep

echo -e "\n-- Done with SignalP --\n"

Command exit status:
2

Command output:

-- Starting with SignalP --

Command error:
flag provided but not defined: -f
Usage of /usr/local/bin/signalp:
-batch int
Number of sequences that the tool will run simultaneously. Decrease or increase size depending on your system memory. (default 10000)
-fasta string
Input file in fasta format.
-format string
Output format. 'long' for generating the predictions with plots, 'short' for the predictions without plots. (default "short")
-gff3
Make gff3 file of processed sequences.
-mature
Make fasta file with mature sequence.
-org string
Organism. Archaea: 'arch', Gram-positive: 'gram+', Gram-negative: 'gram-' or Eukarya: 'euk' (default "euk")
-plot string
Plots output format. When long output selected, choose between 'png', 'eps' or 'none' to get just a tabular file. (default "png")
-prefix string
Output files prefix. (default "Input file prefix")
-stdout
Write the prediction summary to the STDOUT.
-tmp string
Specify temporary file directory. (default "System default tmpdir")
-verbose
Verbose output. Specify '-verbose=false' to avoid printing. (default true)
-version
Prints version.

Work dir:
/data/gn2311/transpi/TransPi/work/a2/ee16086eae55047a892f95dc3fb6cd

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

[PilarLF]

Ey did you solve it?

[sevragorgia]

Hi there,

I think TransPi assumes signalP v4 is available. I think I have a patch to make it run with v5 but will need check. I face lots of problems with v5 due to the way in which signalPv5 handles the paths. For SignalP 6 I have not had any chance to test it but since this is a major redo of signalP it will most likely crash.

Sergio