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

[leehous]

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]

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]

@prvst @fcyu @guoci Hello?

[anesvi]

I think you just email a few hours ago? Give them a bit of time to respond! It is nigh time in Ann Arbor. From: leehous ***@***.***> Sent: Tuesday, April 5, 2022 1:54 AM To: Nesvilab/FragPipe ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [Nesvilab/FragPipe] Error of PeptideProphet (Issue Nesvilab/Crystal-C#11) External Email - Use Caution @prvst<https://github.com/prvst> @fcyu<https://github.com/fcyu> @guoci<https://github.com/guoci> Hello? — Reply to this email directly, view it on GitHub<#11>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM637EI5XXWEFTNQQPODVDPIPTANCNFSM5SRSZVNQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>> ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[anesvi]

You are using a very old version of the tools, which probably explains your crashes FragPipe version 16.0 MSFragger version 3.4 Philosopher version 4.1.0 (build 1635640020) Please upgrade to the latest FragPipe (17.1) and Philosopher 4.1.1 Also, please use one of the default workflows first and a database downloaded by Philosopher. I see you made some unusual changes to MSFragger parameters and also using a custom database. Alexey From: leehous ***@***.***> Sent: Tuesday, April 5, 2022 1:40 AM To: Nesvilab/FragPipe ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [Nesvilab/FragPipe] Error of PeptideProphet (Issue Nesvilab/Crystal-C#11) External Email - Use Caution 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 — Reply to this email directly, view it on GitHub<#11>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM66BB72TJXY7HN2LLG3VDPG3RANCNFSM5SRSZVNQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>> ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[leehous]

Dear anesvi， I'm sorry，I forget the time，I will wait in patience，thank you for responce

…

---- 回复的原邮件 ---- | 发件人 | Alexey ***@***.***> | | 日期 | 2022年04月05日 13:56 | | 收件人 | ***@***.***> | | 抄送至 | ***@***.******@***.***> | | 主题 | Re: [Nesvilab/FragPipe] Error of PeptideProphet (Issue Nesvilab/Crystal-C#11) | I think you just email a few hours ago? Give them a bit of time to respond! It is nigh time in Ann Arbor. From: leehous ***@***.***> Sent: Tuesday, April 5, 2022 1:54 AM To: Nesvilab/FragPipe ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [Nesvilab/FragPipe] Error of PeptideProphet (Issue Nesvilab/Crystal-C#11) External Email - Use Caution @prvst<https://github.com/prvst> @fcyu<https://github.com/fcyu> @guoci<https://github.com/guoci> Hello? — Reply to this email directly, view it on GitHub<#11>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM637EI5XXWEFTNQQPODVDPIPTANCNFSM5SRSZVNQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>> ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[leehous]

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]

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]

Sorry I do not know. Please send us the log from the latest FragPipe. But probably something wrong with your Linux set up. Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: leehous ***@***.***> Sent: Tuesday, April 5, 2022 3:02:17 PM To: Nesvilab/FragPipe ***@***.***> Cc: Nesvizhskii, Alexey ***@***.***>; Comment ***@***.***> Subject: Re: [Nesvilab/FragPipe] Error of PeptideProphet (Issue Nesvilab/Crystal-C#11) External Email - Use Caution 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. — Reply to this email directly, view it on GitHub<#11>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM6YO5JZIIQYRZAOCRGDVDPQPTANCNFSM5SRSZVNQ>. You are receiving this because you commented.Message ID: ***@***.***> ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[leehous]

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

[anesvi]

You are using a custom database and some weird modified open search parameters. I am not saying this is what causing the crash, just I do not understand what you are doing. Perhaps you may need to find another computer to test there. Maybe someone on our FragPipe team would have a clue, but I am not able to help, unfortunately. Alexey From: leehous ***@***.***> Sent: Tuesday, April 5, 2022 3:38 AM To: Nesvilab/FragPipe ***@***.***> Cc: Nesvizhskii, Alexey ***@***.***>; Comment ***@***.***> Subject: Re: [Nesvilab/FragPipe] Error of PeptideProphet (Issue Nesvilab/Crystal-C#11) External Email - Use Caution Here is the log files ,thanks very much professor anesvi! log_2022-04-05_15-14-43.txt<https://github.com/Nesvilab/FragPipe/files/8415949/log_2022-04-05_15-14-43.txt> — Reply to this email directly, view it on GitHub<#11>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM654GYM5UN3QXVEKMX3VDPUUZANCNFSM5SRSZVNQ>. You are receiving this because you commented.Message ID: ***@***.******@***.***>> ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[leehous]

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]

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]

Thanks. We will pay attention to cases where raw file names end with _c Why do you need to change default open search parameters? Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: leehous ***@***.***> Sent: Wednesday, April 6, 2022 12:34:40 PM To: Nesvilab/FragPipe ***@***.***> Cc: Nesvizhskii, Alexey ***@***.***>; Comment ***@***.***> Subject: Re: [Nesvilab/FragPipe] Error of PeptideProphet (Issue Nesvilab/Crystal-C#11) External Email - Use Caution 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<https://github.com/prvst> @fcyu<https://github.com/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. — Reply to this email directly, view it on GitHub<#11>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM6ZZSJBHCNGFHCYBCN3VDUH6BANCNFSM5SRSZVNQ>. You are receiving this because you commented.Message ID: ***@***.***> ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[fcyu]

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