SignalP v6?

[Dikaryotic]

Hi John,

I've got some SingalP6 output I'd like to include in my annotate stage. I've tried the --signalp method but it threw an error. I'm using funannotate v1.8.7. I'll pop in the error then a head of the singalp output file. Maybe you can advise? I suspect it's something to do with the format but can't quite figure it out. Ideally I wouldve liked funannotate to run it natively but it didnt want to pickup the installation.

Existing SignalP results found: Predict/annotate_misc/signalp.results.txt
Traceback (most recent call last):
File "/home/chris/miniconda3/envs/Funannotate/bin/funannotate", line 10, in
sys.exit(main())
File "/home/chris/miniconda3/envs/Funannotate/lib/python3.7/site-packages/funannotate/funannotate.py", line 705, in main
mod.main(arguments)
File "/home/chris/miniconda3/envs/Funannotate/lib/python3.7/site-packages/funannotate/annotate.py", line 963, in main
lib.parseSignalP(signalp_out, secreted_out)
File "/home/chris/miniconda3/envs/Funannotate/lib/python3.7/site-packages/funannotate/library.py", line 5634, in parseSignalP
if col[9] == 'Y': # then there is signal peptide
IndexError: list index out of range

head signalp.results.txt

SignalP-6.0 Organism: Eukarya Timestamp: 20211008163009

ID Prediction OTHER SP(Sec/SPI) CS Position

FUN_000001-T1_FUN_000001 NO_SP 1.000034 0.000000
FUN_000002-T1_FUN_000002 NO_SP 1.000061 0.000000
FUN_000003-T1_FUN_000003 NO_SP 1.000047 0.000000
FUN_000004-T1_FUN_000004 NO_SP 1.000045 0.000000
FUN_000005-T1_FUN_000005 NO_SP 0.999985 0.000069
FUN_000006-T1_FUN_000006 NO_SP 1.000068 0.000000
FUN_000007-T1_FUN_000007 NO_SP 1.000054 0.000000
FUN_000008-T1_FUN_000008 NO_SP 1.000050 0.000001

Cheers,
Chris

[nextgenusfs]

Looks like another new format.... is it tab delimited or space? And what does a "has signal peptide" look like?

[Dikaryotic]

It's tab delimited. Here are the first two identified with signal peptides.

SignalP-6.0 Organism: Eukarya Timestamp: 20211008163009

ID Prediction OTHER SP(Sec/SPI) CS Position

FUN_000010-T1_FUN_000010 SP 0.000237 0.999737 CS pos: 21-22. Pr: 0.9766
FUN_000017-T1_FUN_000017 SP 0.000320 0.999666 CS pos: 25-26. Pr: 0.4228

[nextgenusfs]

Thanks can you attach file so I can make sure the parser gets the last column correctly? I do t want to make any assumptions based on if GitHub stripped any formatting, etc.

[Dikaryotic]

signalp.results.txt

[nextgenusfs]

Thanks. How about the call to signalP v6, this is what is being run on v5:

cmd = ['signalp', '-stdout', '-org', 'euk', '-format', 'short', '-fasta']

Does that still work with v6?

[nextgenusfs]

Parser should be working (I hope) in the master branch, can install with pip to check.

[Dikaryotic]

Hiya,

I've found time again to work on this, I just pulled the new master branch and had a go, I've hit a new error.

: Existing SignalP results found: Predict/annotate_misc/signalp.results.txt
Traceback (most recent call last):
File "/home/chris/miniconda3/envs/Funannotate/bin/funannotate", line 8, in
sys.exit(main())
File "/home/chris/miniconda3/envs/Funannotate/lib/python3.7/site-packages/funannotate/funannotate.py", line 705, in main
mod.main(arguments)
File "/home/chris/miniconda3/envs/Funannotate/lib/python3.7/site-packages/funannotate/annotate.py", line 1002, in main
lib.parseSignalP(signalp_out, secreted_out)
File "/home/chris/miniconda3/envs/Funannotate/lib/python3.7/site-packages/funannotate/library.py", line 5681, in parseSignalP
ID, prediction, score1, score2, position = cols[:5]
ValueError: not enough values to unpack (expected 5, got 4)

[nextgenusfs]

Oh, they must not write the last empty column if there is no hit. That's not very nice of them.... should just be able to put a try/except on that line.

[nextgenusfs]

Okay, can you try with latest in master again and see if it prints any lines to stderr that it cannot parse?

[Dikaryotic]

Heya, looks like it's sort of worked. There appear to be a handful of entries it cannot parse. See below for the output.

Existing SignalP results found: Predict/annotate_misc/signalp.results.txt
signalP parse error: FUN_001618-T1_FUN_001618 SP 0.379709 0.620269
signalP parse error: FUN_001686-T1_FUN_001686 SP 0.491810 0.508172
signalP parse error: FUN_003357-T1_FUN_003357 SP 0.449099 0.550900
signalP parse error: FUN_003817-T1_FUN_003817 SP 0.398018 0.601982
signalP parse error: FUN_004349-T1_FUN_004349 SP 0.432366 0.567619
signalP parse error: FUN_005570-T1_FUN_005570 SP 0.471067 0.528935
signalP parse error: FUN_005972-T1_FUN_005972 SP 0.409434 0.590562
signalP parse error: FUN_008891-T1_FUN_008891 SP 0.363779 0.636212
[Oct 21 02:55 PM]: 697 secretome and 1,949 transmembane annotations added

[Dikaryotic]

Oh, also, I get this when I try to include phobius results. Seems to be some sort of clash. I've run this directly after my last test using --phobius phobius.results.txt

Existing SignalP results found: Predict/annotate_misc/signalp.results.txt
Traceback (most recent call last):
File "/home/chris/miniconda3/envs/Funannotate/bin/funannotate", line 8, in
sys.exit(main())
File "/home/chris/miniconda3/envs/Funannotate/lib/python3.7/site-packages/funannotate/funannotate.py", line 705, in main
mod.main(arguments)
File "/home/chris/miniconda3/envs/Funannotate/lib/python3.7/site-packages/funannotate/annotate.py", line 1019, in main
phobius_out, signalp_out, membrane_out, secreted_out)
File "/home/chris/miniconda3/envs/Funannotate/lib/python3.7/site-packages/funannotate/library.py", line 5746, in parsePhobiusSignalP
if col[9] == 'Y': # then there is signal peptide
IndexError: list index out of range

[nextgenusfs]

Okay thanks. The ones that it can't parse don't have the last column, that must be a bug or something. It is predicting a signal peptide but not the cleavage site?

Second error makes sense I think, let me see what I need to do to make new results work.

[fteufel]

Hey @Dikaryotic , saw this issue by chance, could you provide me with the sequences that show no CS being predicted? This is definitely unexpected behaviour.

[hassantarabai]

Hello,

I recently installed funannotate and it appear the signalp6 pursing error is still there "ValueError: not enough values to unpack (expected 5, got 4)" when passing signalp6 results to funannotate annotate.

Have anybody managed a solution for it ?

[lukaskon]

I am also having the same issue. What is the exact input file type or path supposed to be for --signalp ?

--signalp predict_results/signalp/prediction_results.txt \

Existing SignalP results found: /mnt/ufs18/rs-008/Hausbeck_group/Lukasko/BotrytisDNASeq/CCR7/Predict_Annotate/AI7_fun/annotate_misc/signalp.results.t
xt
-------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/home/lukaskon/anaconda3/envs/funannotate/bin/funannotate", line 10, in <module>
    sys.exit(main())
  File "/mnt/home/lukaskon/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main
    mod.main(arguments)
  File "/mnt/home/lukaskon/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/annotate.py", line 1341, in main
    lib.parseSignalP(signalp_out, secreted_out)
  File "/mnt/home/lukaskon/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/library.py", line 7299, in parseSignalP
    pos = components[2].split("-")[0]
IndexError: list index out of range

[hyphaltip]

would help to have a snapshot of your failed file and what version of funannotate you are running. are you running signalp outside of funannotate then?

I just ran an annotation with signalp6 installed but I think I had to tweak something in the latest code release so you might need to grab code from github to make sure it is all working.

[lukaskon]

I am running funannotate v1.8.15 and yes, signalp6 outside of funannotate.

Here is the annotate log file:
B5_signalp_annotate_slurm.txt
Here are the signalp results from annotate_misc:

signalp.results.txt

If the issue is the signalp file format, maybe I can reformat to make this compatible for the time being.

Let me know if anything else would be helpful. Thank you!