Crystal-C 1.4.4 fails with error message about missing MS1 spectra

[reid-wagner]

When I run Crystal-C 1.4.4 I get the following error message with exit code 1:

Please check if there are MS1 spectra in raw or mzML files.

Crystal-C 1.4.2 runs successfully using the same input data and parameters, so I am guessing those are not the issue.

Because I don't see 1.4.4 published here yet, I'll add that I was originally running it via FragPipe 18.0, although I've also run the isolated java command from FragPipe with the same results.

Let me know if I can provide any further information. Thanks!

[huiyinc]

Hi, I've processed two raw files using FragPipe v18 with Crystal-C 1.4.4 and everything is fine. Which file format are you using, raw, mzML, or mzXML? Is it possible that you share the files with us? Thanks. Huiyin Reid Wagner ***@***.***> 於 2022年6月15日 下午9:31 寫道：  When I run Crystal-C 1.4.4 I get the following error message with exit code 1: Please check if there are MS1 spectra in raw or mzML files. Crystal-C 1.4.2 runs successfully using the same input data and parameters, so I am guessing those are not the issue. Because I don't see 1.4.4 published here yet, I'll add that I was originally running it via FragPipe 18.0, although I've also run the isolated java command from FragPipe with the same results. Let me know if I can provide any further information. Thanks! — Reply to this email directly, view it on GitHub <#8>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALAWWAYCIVOCHQ2F3B3STATVPHLMXANCNFSM5Y3KKKIQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[p-bell]

I have the same issue, running FragPipe v18. Crystal-C version mentioned in pep.xml output: 2019.08

I downloaded the following raw files from PRIDE (PXD034135):
TC-EG_CALU_CoV2_WCL_F23.raw
TC-EG_CALU_CoV2_WCL_F24.raw

Then converted the raw files to mzml using msconvert, and ran open mod searches (each file searched individually):

• TC-EG_CALU_CoV2_WCL_F24.mzml processes without issue.
• TC-EG_CALU_CoV2_WCL_F23.mzml fails with the following error:
  Please check if there are MS1 spectra in raw or mzML files.

Including both files in the same search gives the same error.

Please let me know if I can provide any other info to help resolve the issue.
Thanks

[huiyinc]

Hi Peter, Is it possible that you share the two mzML and fasta files with me so I can take a look of it? Thanks. Huiyin Peter Bell ***@***.***> 於 2022年10月4日 上午8:52 寫道：  I have the same issue, running FragPipe v18. Crystal-C version mentioned in pep.xml output: 2019.08 I downloaded the following raw files from PRIDE (PXD034135): TC-EG_CALU_CoV2_WCL_F23.raw TC-EG_CALU_CoV2_WCL_F24.raw Then converted the raw files to mzml using msconvert, and ran open mod searches (each file searched individually): - TC-EG_CALU_CoV2_WCL_F24.mzml *processes without issue*. - TC-EG_CALU_CoV2_WCL_F23.mzml *fails with the following error*: *Please check if there are MS1 spectra in raw or mzML files.* Including both files in the same search gives the same error. Please let me know if I can provide any other info to help resolve the issue. Thanks — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALAWWAZVRLY72KVDOZNEKKLWBN5UFANCNFSM5Y3KKKIQ> . You are receiving this because you commented.Message ID: ***@***.***>

[p-bell]

Hi Huiyin,

Thanks for getting back to me and looking into the issue.

The files are large (~1.5Gb each) - how is the best way to get them to you? Is the nesvilab account email address ok for me to send a OneDrive link?

Thanks
Pete

[huiyinc]

Hi Peter, Can you please email the OneDrive link to my email address: ***@***.***? Thanks. Huiyin Peter Bell ***@***.***> 於 2022年10月5日 上午1:55 寫道：  Hi Huiyin, Thanks for getting back to me and looking into the issue. The files are large (~1.5Gb each) - how is the best way to get them to you? Is the nesvilab account email address ok for me to send a OneDrive link? Thanks Pete — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALAWWAYDQASBCPRDS3E7CR3WBRVQTANCNFSM5Y3KKKIQ> . You are receiving this because you commented.Message ID: ***@***.***>

[p-bell]

Hi Huiyin, sorry I can't see the email address - it appears as @.*** in the browser.

[huiyinc]

Hi Peter,

Thanks for letting me know. My email address is: [email protected].

Huiyin

[p-bell]

Thanks - the files should be with you now

[huiyinc]

Hi Peter,

I just perform an open search using FragPipe (Crystal-C v.1.4.3) and the fasta/mzML files you sent. The process works fine. Attached is the log file generated by FragPipe. Can you please tell me which version of Crystal-C you use?
Thanks.

Huiyin

log_2022-10-07_15-23-23.txt

[p-bell]

Thanks for looking into it Huiyin.

I also ran it from FragPipe, but it appears to be Crystal-C v.1.4.4 in my installation. (Please see attached log of one of the failed searches):
C:\0-Software\FragPipe-jre-18.0\fragpipe\tools\original-crystalc-1.4.4.jar

Thanks
Pete

log_2022-10-04_17-04-00.txt

[huiyinc]

Hi Peter,

After rechecking Crystal-C and your mzML file, I notice that the library of file reader (batmass-io) is updated to version 1.25.5. In the new version, batmass-io removes MS (MS/MS scans) with no data points. So, a scan (scan number: 91049, TC-EG_CALU_CoV2_WCL_F23.mzML) is excluded (as shown in the attached figure), resulting an exception in Crystal-C.

I have updated Crystal-C to avoid the exception. Can you please download and try the new release? Download link: https://github.com/Nesvilab/Crystal-C/releases/tag/1.5.0

Please feel free to let me know if there is any problem. Thanks.

Huiyin

[p-bell]

Hi Huiyin,

That seems to have solved the problem! Searches of that file now complete successfully :)

Thanks a lot for your help and for continuing to develop these tools.

Cheers
Pete

[p-bell]

Hi again Huiyin,

Sorry I've encountered the same problem with a different file (I'll send by email).

Please would it be possible to take another look?

Thanks
Pete

[huiyinc]

Hi Peter, Sure. Feel free to send me the files. Thanks. Huiyin Peter Bell ***@***.***> 於 2022年10月13日 上午2:12 寫道：  Hi again Huiyin, Sorry I've encountered the same problem with a different file (I'll send by email). Please would it be possible to take another look? Thanks Pete — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALAWWA3UBRF632QUFN2X3J3WC35QVANCNFSM5Y3KKKIQ> . You are receiving this because you commented.Message ID: ***@***.***>

[p-bell]

Thanks Huiyin, I sent the link to the files (Wed 10th) - did you receive it? Please let me know if not and I'll resend.

Cheers
Pete

[huiyinc]

Hi Peter, Sorry for the late reply. After checking the mzML file, I notice that there are 123 MS2 spectra with 0 data points, and that's why Crystal-C fails again. Our group is working on upgrading the file IO library to resolve the issue. A new version of Crystal-C will be released as the new library is complete. We will keep you updated. Thanks. Huiyin Peter Bell ***@***.***> 於 2022年10月15日 週六 上午10:04寫道：

…

Thanks Huiyin, I sent the link to the files (Wed 10th) - did you receive it? Please let me know if not and I'll resend. Cheers Pete — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALAWWA2XQUATYWXV6G2ZEYDWDIGKLANCNFSM5Y3KKKIQ> . You are receiving this because you commented.Message ID: ***@***.***>

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

[p-bell]

Thanks for looking into it Huiyin.

I look forward to using the new version when it's ready.

Thanks again,
Pete