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Nesvilab / FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
http://fragpipe.nesvilab.org
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Peaks with unreasonable large mz broke MSFragger #1610

Open amingson opened 3 weeks ago

amingson commented 3 weeks ago

- Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.) log_2024-06-04_19-16-51.txt

- Describe the issue or question:

Dear Author,

I hope this message finds you well.

I am currently encountering an error while running Fragger. Upon reviewing the logs, I have not been able to identify any potential causes for this issue. I would greatly appreciate your assistance in resolving this matter.

Thank you in advance for your help.

Sincerely,

Anler

fcyu commented 3 weeks ago

Hi Anler,

Thanks for the bug report. Could you share 20170311_QEh1_LC2_FaMaChCh_SA_HLApI_3912-BAM_1_R1.raw and 2024-05-23-decoys-contam-Noncoding_ref.fasta.fas with us? I need the files to figure out the cause of the error.

Here is the link to upload the file: https://www.dropbox.com/request/9BRiumEKInjtm1ie1CNU

Thanks,

Fengchao

amingson commented 3 weeks ago

Hi Anler,

Thanks for the bug report. Could you share 20170311_QEh1_LC2_FaMaChCh_SA_HLApI_3912-BAM_1_R1.raw and 2024-05-23-decoys-contam-Noncoding_ref.fasta.fas with us? I need the files to figure out the cause of the error.

Here is the link to upload the file: https://www.dropbox.com/request/9BRiumEKInjtm1ie1CNU

Thanks,

Fengchao

Thank you. I have uploaded the file.

Best,

Anler

fcyu commented 3 weeks ago

Hi Anler,

Thanks for sharing the file. The error was because there were MS2 peaks with unreasonable large m/z.

image

I have added a filter to remove those peaks since it makes no sense to keep them. Send an email to yufeATumich.edu (replace AT with @) if you want to use a pre-released version of MSFragger.

Best,

Fengchao

amingson commented 2 weeks ago

Hi Anler,

Thanks for sharing the file. The error was because there were MS2 peaks with unreasonable large m/z.

image

I have added a filter to remove those peaks since it makes no sense to keep them. Send an email to yufeATumich.edu (replace AT with @) if you want to use a pre-released version of MSFragger.

Best,

Fengchao

Dear Author,

Thank you so much for your assistance. I have been quite busy these past few days and just now had the time to respond to your message. I hope you don't mind. I have sent you an email requesting the pre-released version.

Best regards,

Anler