Replies: 3 comments 1 reply
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Yes, those warnings can be ignored
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From: JUMPSuite ***@***.***>
Sent: Wednesday, February 23, 2022 2:10:34 AM
To: Nesvilab/philosopher ***@***.***>
Cc: Subscribed ***@***.***>
Subject: [Nesvilab/philosopher] "cannot open data file ..." warning in peptideprophet (Discussion #318)
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Hi there,
I'd like to ask a question about philosopher-peptideprophet.
According to the tutorial of FragPipe in Linux (https://fragpipe.nesvilab.org/docs/tutorial_linux.html), peptideprophet was executed after moving pepXML file(s) to the working directory (i.e., workspace). However, in this case, though peptideprophet generated an output file (pep.xml file), it produced warnings as follows,
...
file 1: /home/usr/FragPipe/test/test.pepXML
WARNING: cannot open data file /home/usr/FragPipe/test/test.mzML in msms_run_summary tag... trying .mzXML ...
WARNING: CANNOT correct data file /home/usr/FragPipe/test/test.mzXML in msms_run_summary tag...
WARNING: cannot open data file /home/usr/FragPipe/test/test.mzML in msms_run_summary tag... trying .mzXML ...
WARNING: CANNOT correct data file /home/usr/FragPipe/test/test.mzXML in msms_run_summary tag...
processed altogether 20318 results
INFO: Results written to file: /home/usr/FragPipe/test/interact-test.pep.xml
...
By the way, when I followed the procedure (https://github.com/Nesvilab/philosopher/wiki/Simple-Data-Analysis), it did not produce the above warnings. The pep.xml file is identical to the above one.
May I simply ignore those warnings? If so, could you please make philosopher not generate such warnings?
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Thank you for your quick response. Let me ask another question related to the warning. INFO[11:00:59] Executing PeptideProphet v4.1.1
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These warnings are useless. They try to correct some scan numbers or something, from some issue 10 years ago. Just ignore
You do not even need to use peptideprophet (unless open search). Our default is Percolator now
Alexey
From: JUMPSuite ***@***.***>
Sent: Wednesday, February 23, 2022 12:12 PM
To: Nesvilab/philosopher ***@***.***>
Cc: Nesvizhskii, Alexey ***@***.***>; Comment ***@***.***>
Subject: Re: [Nesvilab/philosopher] "cannot open data file ..." warning in peptideprophet (Discussion #318)
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Thank you for your quick response. Let me ask another question related to the warning.
When I tried to process a Bruker .d file (ddaPASEF data), I had the warnings even though I ran MSFragger and philosopher in the same directory (i.e., similar to https://github.com/Nesvilab/philosopher/wiki/Simple-Data-Analysis). In spite of those warnings, peptideprophet, proteinprophet, filtering and report generation were done. May I still ignore them? I wonder why it happened to Bruker .d files (no warnings for mzML files as described above).
INFO[11:00:59] Executing PeptideProphet v4.1.1
file 1: /home/usr/Data/Bruker/bruker_test.pepXML
Unknown file type. No file loaded./home/usr/Data/Bruker/bruker_test.d
WARNING: cannot open data file /home/usr/Data/Bruker/bruker_test.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ...
WARNING: CANNOT correct data file /home/usr/Data/Bruker/bruker_test.mzML in msms_run_summary tag...
Unknown file type. No file loaded./home/usr/Data/Bruker/bruker_test.d
WARNING: cannot open data file /home/usr/Data/Bruker/bruker_test.d in msms_run_summary tag... unrecognized extension .d, trying .mzML ...
WARNING: CANNOT correct data file /home/usr/Data/Bruker/bruker_test.mzML in msms_run_summary tag...
processed altogether 18072 results
INFO: Results written to file: /home/usr/Data/Bruker/interact-bruker_test.pep.xml
* /home/usr/Data/Bruker/interact-bruker_test.pep.xml
* Building Commentz-Walter keyword tree...
* Searching the tree...
* Linking duplicate entries...
* Printing results...
...
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Thank you for the clarification. |
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Hi there,
I'd like to ask a question about philosopher-peptideprophet.
According to the tutorial of FragPipe in Linux (https://fragpipe.nesvilab.org/docs/tutorial_linux.html), peptideprophet was executed after moving pepXML file(s) to the working directory (i.e., workspace). However, in this case, though peptideprophet generated an output file (pep.xml file), it produced warnings as follows,
...
file 1: /home/usr/FragPipe/test/test.pepXML
WARNING: cannot open data file /home/usr/FragPipe/test/test.mzML in msms_run_summary tag... trying .mzXML ...
WARNING: CANNOT correct data file /home/usr/FragPipe/test/test.mzXML in msms_run_summary tag...
WARNING: cannot open data file /home/usr/FragPipe/test/test.mzML in msms_run_summary tag... trying .mzXML ...
WARNING: CANNOT correct data file /home/usr/FragPipe/test/test.mzXML in msms_run_summary tag...
processed altogether 20318 results
INFO: Results written to file: /home/usr/FragPipe/test/interact-test.pep.xml
...
By the way, when I followed the procedure (https://github.com/Nesvilab/philosopher/wiki/Simple-Data-Analysis), it did not produce the above warnings. The pep.xml file is identical to the above one.
May I simply ignore those warnings? If so, could you please make philosopher not generate such warnings?
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