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bzhanglab / PepQuery

PepQuery: a targeted peptide search engine
http://pepquery.org
GNU General Public License v3.0
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Exception in thread "main" java.lang.NumberFormatException: For input string: "peptide" #77

Open Seb-Leb opened 3 weeks ago

Seb-Leb commented 3 weeks ago

I am getting an error that I dont understand, could you advise? The input search is a list of peptide and spectrum scan numbers separated by a tab character... (I tried to add "controllerType=0 controllerNumber=1 scan=" in front of the scan number to match the spectrum title, but it gave the same error...) thank you!

PepQuery command: -itol 0.05 -hc TRUE -cpu 4 -t peptide -i query_file.txt -e 1 -varMod 117 -maxVar 3 -db tools/uniprot_swissprot_human_2016.fasta -ms spectra.mgf -o outdir

query file:

GREDGELEEGELEDDGAEETQDTSGGPER   12095
NDDIPEQDSLGLSNLQK   17936
MAVAMVK 12715
ATDGMGEGKTAGLGASDCGRAGR 20163

Spectra file:

>head spectra.mgf
BEGIN IONS
TITLE=controllerType=0 controllerNumber=1 scan=3
SCANS=3
RTINSECONDS=0.895778864
PEPMASS=832.240417480469
CHARGE=2+
122.2260666 4.0869851112
122.9780350 1.9533622265
124.1365204 1.9854439497
144.0026703 7.8467755318

output:

Exception in thread "main" java.lang.NumberFormatException: For input string: "peptide"
    at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67)
    at java.base/java.lang.Integer.parseInt(Integer.java:668)
    at java.base/java.lang.Integer.valueOf(Integer.java:999)
    at main.java.pg.PeptideSearchMT.main(PeptideSearchMT.java:381)
wenbostar commented 3 weeks ago

Could you please try to use spectrum title in the mgf file as the spectrum ID in your query_file.txt file and add parameter "-indexType 2" as well? If this doesn't work, could you share the three input files with me?

Seb-Leb commented 2 weeks ago

Thank you Bo! I tried with the parameter you sent but it still gives the same error. Here is the full command I use: java -Xmx16g -jar pepquery-2.0.2/pepquery-2.0.2.jar -indexType 2 -itol 0.05 -hc TRUE -cpu 4 -t peptide -i pepq_bug/spectra.mgf -e 1 -varMod 117 -maxVar 3 -db pepq_bug/uniprot_swissprot_human_2016.fasta -ms pepq_bug/spectra.mgf -o pepq_bug

I zipped all the relevant files in here: https://drive.google.com/file/d/1Nbw7b5JuSGGjg8o-QoKuCIejLjGu0YFx/view?usp=sharing

Seb-Leb commented 1 week ago

I tried changing the spectrum titles to have only the scan numbers, but it still doesn't work...

wenbostar commented 1 week ago

I will look at this issue today and get back to you soon.

Seb-Leb commented 6 days ago

excellent! thank you!

Seb

From: Bo @.> Sent: October 29, 2024 13:30 To: bzhanglab/PepQuery @.> Cc: Sébastien Leblanc @.>; Author @.> Subject: Re: [bzhanglab/PepQuery] Exception in thread "main" java.lang.NumberFormatException: For input string: "peptide" (Issue #77)

I will look at this issue today and get back to you soon.

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