search

Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
Other
184 stars 37 forks source link

MSFragger MBR Error #343

Closed BenSamy2020 closed 3 years ago

BenSamy2020 commented 3 years ago

Greetings,

I am currently performing close search - IonQuant - MBR. I am consistently experiencing failed runs. I am experiencing the error of: _2021-04-01 00:44:13 [ERROR] - Protein sp|Q4VXU2|PAP1L_HUMAN from D:\Parthiban\RAW_MS_Files\Malaria\Clinical_malaria_Main_Study_Raw_Files\20210223_MalariaS22-1/protein.tsv cannot be found from any psm.tsv.

I have attached the MSfragger log file here for your reference. Lastly, I would like to thank you for providing this amazing open-source software and your assistances with troubleshooting.

Regards, Ben

log_2021-04-01_01-07-15.txt

fcyu commented 3 years ago

Hi Ben,

We have fixed this issue in the latest version. Could you upgrade your FragPipe to 15.0?

Best,

Fengchao

BenSamy2020 commented 3 years ago

Greetings FengChao,

I am still facing the error with the updated version of FragPipe. I have attached the log file for your reference.

Regards, Ben log_2021-04-01_11-50-20.txt

fcyu commented 3 years ago

Hi Ben,

Can you send all of your files except for the raw files to me? I can give you a link to upload if you don't have a way to send those files.

Best,

Fengchao

BenSamy2020 commented 3 years ago

Greetings FengChao,

I deleted all the files in the directory. But I am re-running the search again. Also can you provide me a link. When I have obtained all the files, I will upload it onto the link that you provided me.

Sorry for the delay.

Regards, Ben

fcyu commented 3 years ago

Thanks Ben,

Here is the link: https://www.dropbox.com/request/wYNFAHHMfZAfTZrGL8sT

Best,

Fengchao

BenSamy2020 commented 3 years ago

Greetings FengChao,

I have successfully uploaded all files expect for the raw files.

Regards, Ben

fcyu commented 3 years ago

Hi Ben,

Those files are well received. The files looks OK. To reproduce the error, could you also send me your raw files and fasta files?

Thanks,

Fengchao

BenSamy2020 commented 3 years ago

Greetings,

There are 60 raw files. It's going to be about 60GB. Can I send it to the same drop box link?

Regards, Ben

fcyu commented 3 years ago

Yes, thanks.

Best,

Fengchao

BenSamy2020 commented 3 years ago

Greetings FengChao,

The files will take 4000 mins (~66 hours) to get uploaded. I have successfully transferred the protein database file. Will update you once the files had been successfully uploaded.

Currently, is there any other way to troubleshoot this error?

Regards, Ben

fcyu commented 3 years ago

Hi Ben,

You can convert the raw to mzml format using the tutorial (https://msfragger.nesvilab.org/tutorial_convert.html) to reduce the size.

You can also use the database downloaded by Philosopher (which is from UniProt) to see if the error is still there.

Best,

Fengchao

anesvi commented 3 years ago

Try on a smaller number of files too, to see if you can get the same error. And yes, using philosopher downloaded database is a good idea, there are some incompatibilities with custom databases observed occasionally

Sent from my iPhone

On Apr 1, 2021, at 8:27 PM, Fengchao @.***> wrote:

 External Email - Use Caution

Hi Ben,

You can convert the raw to mzml format using the tutorial (https://msfragger.nesvilab.org/tutorial_convert.html) to reduce the size.

You can also use the database downloaded by Philosopher (which is from UniProt) to see if the error is still there.

Best,

Fengchao

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/343#issuecomment-812248252, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM66FMIWSWRK4L2OKBALTGUFMDANCNFSM42E4EC7A.

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

BenSamy2020 commented 3 years ago

Greetings FengChao and Alexey,

I had to switch to a high-speed internet connection and had successfully uploaded the .raw files for your investigation. Concurrently, I will test the philosopher downloaded database.

On a side note, the searching of the file using MSFragger is faster compared to uploading...

Regards, Ben

fcyu commented 3 years ago

Hi Ben,

Thanks. I will let you know as soon as I find something.

Best,

Fengchao

BenSamy2020 commented 3 years ago

Greetings Alexey and FengChao,

You guys are spot on. After downloading the protein database directly via FragPipe interface, my searches went fine. Thanks alot!

Also I am planning to perform searches using a non-UniProt protein database: https://www.openprot.org/p/download By any chance is there a way to make this database compatible with FragPipe?

Regards, Ben

Non-UniProt_Protein_Database

fcyu commented 3 years ago

Hi Ben,

Sorry for the late reply.

We were fixing this bug and adding one more functionality (i.e., If the experiment names start with lib, IonQuant will use the runs as library runs: not transfer ions to them in MBR and not include them in MaxLFQ). Could you try the pre-release version from https://www.dropbox.com/s/l6ruycbcdc47ybr/FragPipe-15.1-build4.zip?dl=0 with your OpenProt database to see if the bug is fixed?

Best,

Fengchao

BenSamy2020 commented 3 years ago

Greetings @fcyu,

Currently I am searching some backlog data on FragPipe V15.0. Once all the searches are done, I will download the above pre-release and test out IonQuant-MBR with OpenProt database.

Also is the OpenProt database format suitable with FragPipe?

Regards, Ben

fcyu commented 3 years ago

According to combined_protein.tsv, Philosopher cannot recognize some of the proteins' Protein ID, Entry Name, and Gene Name, Organism, and Description. Other than that, the result looks fine.

Best,

Fengchao

BenSamy2020 commented 3 years ago

Greetings @fcyu,

With the update FragPipe, I am not facing any IonQuant MBR search issues. Thank you.

Regards, Ben