Issue with replicating isobaric tags test in docker

[caroott]

I'm currently trying to get the docker version of PyQuant to work at my pc. As a test, i tried to replicate the method in integration_isobaric_tags.py in the test folder of the repository with the data given there. The command i ran in docker was:

docker run -v C:/Users/jonat/source/repos/pyquant/tests/data:/data chrismit7/pyquant:v0.2.3-rc2 --scan-file /data/iTRAQ_Data.mzML -o /data/itraq_test --precursor-ppm 200 --isobaric-tags --label-scheme /data/itraq_labels.tsv

The output in the console was the following:

msparser not found, Mascot DAT files unable to be parsed
Loading Scans:

Scans loaded.
Beginning quantification.

After executing the command, a itraq_test.tmp file appeared with a size of 0 kb. I let it run over night, and the size of the .tmp file didn't change and nothing else happened, indicating that the application was stuck.
My question now is, am I missing something in my execution, or is there an issue with the docker container? Thanks in advance for any help!

[Chris7]

The data is stored in git LFS, can you make sure the files were actually downloaded? Those files/tests are part of the travis tests, so they run all the time.

[jdlab8]

Hello, I am just following up to see if anyone has found a solution to this? I believe I am experiencing a similar issue with my data. The command I wrote in docker:
C:\Users\Jerry>docker run -v C:/Users/PyQuant/data/:/data/ chrismit7/pyquant --tsv /data/evidence_PKO14.txt --peptide-col "Sequence" --rt "Retention time" --mz "m/z" --scan-col "MS/MS Scan Number" --charge "Charge" --source "Raw file" --label-scheme /data/d3leucine.tsv --out /data/evidenceoutput --maxquant

My output was similar where a tmp file of size 0kb appears after running overnight:
msparser not found, Mascot DAT files unable to be parsed Loading Scans: .............. Scans loaded. Beginning quantification. Processing /data/PKO_D14_1.mzML. ........................

I would really appreciate any help on this. Thank you!

[Chris7]

My only guess is something with Windows or the docker VM you are running. I ran the docker image this morning against the test data without any issues.

docker run -v /home/chris/Devel/pyquant/label_templates/:/templates -v /home/chris/Devel/pyquant/tests/data/:/data/ chrismit7/pyquant --tsv /data/ecoli_mq_124_evidence.txt --label-scheme /templates/maxquant_3state.tsv --out /data/evidenceoutput --maxquant

If you upload your data somewhere I could see if it reproduces on my end. Also, if you provide the --maxquant flag, you do not need to pass in the column information.

[Chris7]

I think the issue here is docker is not being run in interactive mode, so the output (pyquant tries to stream it using an inplace method to rewrite the output), is not being returned.

Unfortunately, this also includes error messages. Try running with the -it flag as well. I'll need to update the docs to recommend this as well.