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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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DIANN_v1.9.1_only first search report, no final pg_report #1183

Open PsuperGirl opened 2 months ago

PsuperGirl commented 2 months ago

Dear Vadim,

For my ongoing study, I have been using the HPC cluster (Linux) to quantify my data with DIANN1.9.1. I transferred the script generated from the Windows interface, but I’ve encountered an issue: I only received the report for the first search, and it appears that the second search did not start at all.

Diann-67828_report-first-pass.manifest.txt report-first-pass.manifest.txt Diann-67828_report-first-pass.parquet report-first-pass.parquet Diann-67828_report-first-pass.pr_matrix.tsv report-first-pass.pr_matrix.tsv Diann-67828_report-first-pass.tsv report-first-pass.tsv

Here I attached the script I used on our cluster and also the output in the cmd. Is that possible for you to check it out? I would appreciate any insights or suggestions on how to troubleshoot this issue.

Thank you very much for your help.

Best, JJ

Screenshot 2024-09-23 at 13 45 15

DIANN_cluster_script.txt

vdemichev commented 1 month ago

Hi JJ,

This is a known issue in 1.9.1 on Linux, i.e. the matrix generation need to be turned off, otherwise it exits when generating matrices and therefore does not proceed to the second pass. This is fixed now, i.e. will work as expected in the 1.9.2.

Best Regards, Vadim

PsuperGirl commented 1 month ago

Hi Vadim, Thank you very much for your clarification. Does that mean I will still get the final report even I turn off the matrix generation?

Best, JJ

vdemichev commented 1 month ago

Yes, the main report is always generated.

PsuperGirl commented 1 month ago

Thank you very much. Will v1.9.2 be able to read the .quant file generated by v1.9.1?

vdemichev commented 1 month ago

No, .quant files are version-specific.

PsuperGirl commented 1 month ago

Thanks a lot. I have updated my script and restarted the analysis. I could not find v1.9.2 released. Is it not released yet?

PsuperGirl commented 1 month ago

Dear Vadim,

The analysis has finished with modified script where "-matrixes" was turned off. However, I did not get pg.matrix because I turned off this option in order to start the second pass. Here are all the reports I got. Is it how I should expect?

Diann-67841_report-first-pass.parquet
Diann-67841_report.tsv Diann-67841_report-first-pass.stats.tsv Diann-67841_report-first-pass.tsv
Diann-67841_report.log.txt
Diann-67841_report.parquet
Diann-67841_report.stats.tsv

I am wondering if I could use this PG.quantity information in this matrix "Diann-67841_report.tsv" to do further data analysis.

Best, JJ