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Crystal-C can't generate the new *_c.pepXML file if the run name ending with _c #11

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leehous opened this issue Apr 5, 2022 · 14 comments
Open

Crystal-C can't generate the new *_c.pepXML file if the run name ending with _c #11

leehous opened this issue Apr 5, 2022 · 14 comments
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@guoci

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@leehous
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leehous commented Apr 5, 2022

I encountered some unusual problems， when I use fragpipe to analysis a batch of .raw files, the same parameters on different computers sometimes return error as "This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::ios_base::failure[abi:cxx11] >'
: iostream error
Process 'PeptideProphet' finished, exit code: 1
Process returned non-zero exit code, stopping"

I have read similiar questions on ISSUES, while the solution you provided can't resolve this problem, I have tried to analysis single rawfiles each time, while the error seems random, not happens every time. Could you please give me some advice? Thankyou very much

The log file is provided as follows:
log_2020-11-03_12-34-19.txt
@leehous
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leehous commented Apr 5, 2022

or sometimes it is "terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::ios_base::failure[abi:cxx11] >'
what(): failed opening file: The system cannot find the file specified.​

: iostream error
FATA[13:28:03] Cannot execute program. there was an error with PeptideProphet, please check your parameters and input files
Process 'PeptideProphet' finished, exit code: 1
Process returned non-zero exit code, stopping

Cancelling 21 remaining tasks
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet"
[log_2022-04-05_13-39-24.txt](https://github.com/Nesvilab/FragPipe/files/8415154/log_2022-04-05_13-39-24.txt)

log files as follows, I checked the parameters repeatedly, while didn't find any wrong could cause this error

@leehous
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leehous commented Apr 5, 2022

@prvst @fcyu @guoci Hello?

@anesvi
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anesvi commented Apr 5, 2022 via email

@anesvi
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anesvi commented Apr 5, 2022 via email

@leehous
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leehous commented Apr 5, 2022 via email

@leehous
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leehous commented Apr 5, 2022

While, the version i use is exactly older, while I noticed that the error not happens every time. Do you mean that this is the source code, which is not suitable for the computer environment I provide?

@leehous
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leehous commented Apr 5, 2022

Dear professor anesvi,
I have updated the Fragpipe and philosopher version as your advice, while the error still appears, do you have any suggestions about parameters? The error I meet is really weird.

@anesvi
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anesvi commented Apr 5, 2022 via email

@leehous
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leehous commented Apr 5, 2022

Here is the log files ,thanks very much professor anesvi!
log_2022-04-05_15-14-43.txt

@anesvi
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anesvi commented Apr 5, 2022 via email

@leehous
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leehous commented Apr 5, 2022

Thank you for your sugggestions, professor anesvi. In fact，I just modified limited parameters, such as LOS, missed cleveages, precursor lower limits ,checked crystal-C and PTM-shepred, do you mean that these changes are not appropriate for open search workflow?

@leehous
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leehous commented Apr 6, 2022

I think I figured out the reason. When I analysis a raw file names with "_c", the crystal-C validation couldn't output corresponding pepxml files suffixed with "_c", then no input files would be identified and read by peptideprophet. After I tried to change the suffix to "_e","_g",etc., the program could run smoothly. This may be caused by some small problems in the source code， and lastest fragpipe and philosopher seems didn't resolve this, I hope my feedback can be helpful to you @prvst @fcyu
Finally, thank you very much for your patience. I still hope you can answer the question of my open search parameters. I'm a little worried about my parameters.

@anesvi
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anesvi commented Apr 6, 2022 via email

@fcyu
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fcyu commented Apr 6, 2022

Hi @leehous ,

Thank you very much for your testing and feedback.

Hi Alexey,

When I analysis a raw file names with "_c", the crystal-C validation couldn't output corresponding pepxml files suffixed with "_c", then no input files would be identified and read by peptideprophet.

Is that something we should fix in Crystal-C?

Best,

Fengchao

@fcyu fcyu unassigned prvst Apr 6, 2022
@leehous leehous closed this as completed Apr 6, 2022
@fcyu fcyu reopened this Apr 6, 2022
@fcyu fcyu mentioned this issue Jun 21, 2022
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@fcyu fcyu changed the title Error of PeptideProphet Crystal-C can't generate the new *_c.pepXML file if the run name ending with _c Jun 21, 2022
@fcyu fcyu transferred this issue from Nesvilab/FragPipe May 31, 2023
@guoci guoci mentioned this issue Jun 1, 2023
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@prvst @guoci @fcyu @anesvi @leehous