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Old 04-11-2018, 04:30 AM   #1
duna
Junior Member
 
Location: italy

Join Date: Apr 2018
Posts: 1
Default problem with signalP not working

Hello everybody, and thank you to have accepted me in the forum!

I am trying to make signalP 4.1 working on iOS 10.13.3 since days and I hope that someone can help me

I downloaded the package for the darwin system and followed the installation instructions. But when I made the test

> ./signalp -t euk -f short test/euk10.fsa > euk10.fsa.short_out

I obtained a different output then expected

----
# SignalP-4.1 euk predictions
# Measure Position Value Cutoff signal peptide?
max. C 1 0.000
max. Y 1 0.000
max. S 1 0.000
mean S 1-0 0.000
D 1-0 0.000 0.450 NO
Name= SP='NO' D=0.000 D-cutoff=0.450 Networks=SignalP-noTM
---

and the same if I test a home made file of amminoacid contigs like this

---
>a
QKMKFKFVYILQYNYNCTSLQKNDKIALFSLPPTLSANGGVSLIKRGWHEIPEIMCCLGMIGISTVFLGISIVRYDADLNHQYKFQYTVVRDTDVRDEWVKKKMYN
>b
LLLITRVHHSSPTVFSTSYARYYATVLGCLVVHFLLHPFVPHISVSNHCVLKFVLVIQVCVVADNTNSQEHS
>c
TRVFSRIELAGERLNCPAAFPLHVSTSTVQTVQKAERRTAPPPLRLATTLGSRPAGHQGQHYSPLPHP
>d
KIPSSCRSVESCICCIEGVLAWKVCSPRANAEIETERESETESETEKETDRQTDRQTDRQTDRETKTDRKTKTD
>e
KGRGLAGYEPAYSHVLNWQANVLTVLPLSPFMSVQVPSRQYKKPKDVLPLRPSDLPQPWAADQPDIKVSTTVPYLIPKDGQDDQVKQTLTLATFVERYPLAVEAWSHVYVVLRVYWRGRCALHGQMPK
>f
ASGKRRPLSQPSGDPSSQMVHLNSQSFPNTPYRNEMKVTLLGRIGKIGMLSGIWQTGGIGQWPNA
>g
TAGSQVYPEVYLPSGKCPEIRCMRLKRGRYHMNLWGNFTGPT
>h
LAMKVSSVLTTGEWPYRFIPDLSRDSLAMKVSSGLTTGEWPYRFIPDLSRDSLAMKVSSALTTGEWPYRFIPDLSRDSLAMKVSSGLTTGEWPYRFIPDLSRDSLAMKVSS
----

with this command

./signalp -t euk -f short /path/prova2.fasta > /path/output.txt

I get this output file

----
# SignalP-4.1 euk predictions
# name Cmax pos Ymax pos Smax pos Smean D ? Dmaxcut Networks-used
0.000 1 0.000 1 0.000 1 0.000 0.000 N 0.450 SignalP-noTM
----

but no error message appeared... someone know what can be the problem?

Thank you for any help!
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