philosophers on Linux analysis for AP-MS data

[prvst]

Discussed in #277

^{Originally posted by Bin-cc September 27, 2021}
Hi,

Thank you for doing such an outstanding work. There are some questions I would like to ask you. I've run into some problems running philosopher on a compute cluster (CentOS 7 Linux). The philosopher.yml and comet.params are referenced from this. And the log is as follows.

time="14:58:00" level=info msg="Executing Pipeline  v4.0.0"
time="14:58:00" level=info msg="Creating workspace"
time="14:58:00" level=warning msg="A meta data folder was found and will not be overwritten. "
time="14:58:00" level=info msg="Initiating the workspace on /bin/A1BG/A1BG_1"
time="14:58:00" level=info msg="Creating workspace"
time="14:58:00" level=warning msg="A meta data folder was found and will not be overwritten. "
time="14:58:00" level=info msg="Initiating the workspace on /bin/A1BG/A1BG_2"
time="14:58:00" level=info msg="Creating workspace"
time="14:58:00" level=warning msg="A meta data folder was found and will not be overwritten. "
time="14:58:00" level=info msg="Annotating the database"
time="14:58:12" level=info msg="Running the Database Search"
time="14:58:12" level=fatal msg="Missing parameter file or data file for analysis. "

The reason seems to be that the system cannot find my comet.params or .mzml file. I'm sure my file path is fine. The same operation I have successfully implemented on Windows, but for some reason I am having problems on Linux. I was a little confused as to why this was the case. Thank you!

Best ragards,

Bin

[sarah-haynes]

Hi Bin, regarding the latest issue:

The problem of .meta/razor.bin is indeed solved. Thank you. But instead, I enconuter a new problem as follows.
INFO[13:56:23] Protein inference results decoy=20 target=4202
INFO[13:56:23] Converged to 0.08 % FDR with 1238 Proteins decoy=1 threshold=0.9975 total=1239
2021/11/20 13:56:24 RemoveAll .: invalid argument
I can get combined.pep.xml and combined.prot.xml, but .tsv are not generated. I'm sure it's with the latest .yml and comet.params, and set the parameters as you said. What else should I do?

Can you confirm that you're running this set of commands on multiple sub-folders, each containing different spectral files?

--Sarah

[prvst]

@Bin-cc can you share your whole data with us?

[prvst]

Scratch that, we implemented a fix for your issue, a new version will be out soon. Thanks for reporting,

[Bin-cc]

Dear Philosopher group, I had tried again in a new and clean workspace and changed Protein Inference to no. However, I still encounter the same problem. INFO[11:02:45] Protein inference results decoy=20 target=4206 INFO[11:02:45] Converged to 1.03 % FDR with 1549 Proteins decoy=16 threshold=0.9197 total=1565 2022/01/05 11:02:46 RemoveAll .: invalid argument I changed my data and database, but before using the latest version, I had tested it with v3. 4. 13 and ran it successfully. I'm also wondering why I can't run it successfully with the latest version, so I attach my data and database to you, could you use it to test again? The parameters from philosopher.yml and comet.param are default. Thank you for helping me find the root of the problem. Best regards, Bin test.zip <https://drive.google.com/file/d/1bB_Y7-QJaICU2C5uF9wuqyDwvN0-DL25/view?usp=drive_web> Felipe da Veiga Leprevost ***@***.***> 于2022年1月5日周三 00:32写道：

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[prvst]

@Bin-cc We added a fix to your issue into the latest version, soon to be released. Thanks for reporting.

Fixed. Added to v4.2.1.

[fcgportal]

Hi there, I am facing the same problems. Is there any way to solve it? Thanks so much.

[Bin-cc]

Hi, I'm still waiting for the latest version and have no idea about it.

Hi there, I am facing the same problems. Is there any way to solve it? Thanks so much.

[prvst]

We added some extensive changes to the program the require more testing, but we should have something soon, thanks for being patient.