MaxQuant v2.7.0 does not start run in Linux

[gitMakeCoffee]

I recently downloaded MaxQuant v2.7.0 on both my Windows machine and on a Linux cluster. The MaxQuant GUI opens fine on Windows. On Linux, running dotnet MaxQuantCmd.dll --help does output the command help.

I created an XML file using the Windows GUI, and uploaded it to the Linux cluster (only one RAW file, phosphoproteomics from HeLa cells). After changing the path to the FASTA file and the RAW Thermo file, I tried running MaxQuant on the Linux compute node. When running the command, no progress/output is shown (no text output). However, when adding the -n flag, the dry run does show all the steps in the pipeline (please find the output of the dry run below). The RAW file is not corrupted.

I am running MaxQuant v2.7.0, with .NET SDK v8.0.412, and Mono v6.12.0.122.

Any idea what the issue might be?
Is it still possible to download older versions?
Thanks.

[comaecliptic]

Hello! Thanks for reaching out. I have a few questions: Were there no new files or folders produced in the folder with the raw file as well? Were you able to successfully launch older versions of MQ on the Linux machine? If you make this run on Windows, does it launch successfully?
Also, can you upload an mqpar.xml file somewhere, so I can take a look?

[gitMakeCoffee]

Hello,

Thank you for the quick reply. Here are the answers to your questions:

• Were there no new files or folders produced in the folder with the raw file as well?
  I left the software running for 20h, the terminal was still blank. The command did create an index for the single input raw file, and a combined folder :

• Were you able to successfully launch older versions of MQ on the Linux machine?
  I unfortunately do not have access to older versions. Is there a way to download those from the website? The form only allows me to download the latest version. Would you be able to share a link?
• If you make this run on Windows, does it launch successfully?
  I will try this tomorrow morning for sure. However I will not have significant computing power... Is 4 threads + 4 GB RAM enough for one sample?
• Also, can you upload an mqpar.xml file somewhere, so I can take a look?
  Please check your inbox.

Thanks again

[comaecliptic]

• Hm, interesting that proc folder is empty, usually it is the place where error messages are written.
• It doesn't make sense to try older MaxQuant versions if you haven't tried them before; they should be the same in terms of working on Linux.
• It should be fine if the raw file is not very big, though I would limit the threads to 1 in MQ if that's the case.
• Thanks! I don't see anything out of order there. Can you also share the command you use to launch MQ in Linux?
• Also, just in case, you seem to be using a non-standard FASTA file, can you check that the identifier rule is fine? You can use the "Test" button here:

[comaecliptic]

Oh, I think I know what the problem is. You have LFQ turned on, but only 1 sample, which prevents MQ from starting entirely. You just need to turn off LFQ.

[gitMakeCoffee]

Hello,

Sorry for the delay. Here are my answers:

• Thanks! I don't see anything out of order there. Can you also share the command you use to launch MQ in Linux?

dotnet maxquant_v2.7.0.0/bin/MaxQuantCmd.dll params.xml

• Also, just in case, you seem to be using a non-standard FASTA file, can you check that the identifier rule is fine?

I think it's fine. I downloaded the FASTA from Uniprot. Here's the result of the Test button.

• Oh, I think I know what the problem is. You have LFQ turned on, but only 1 sample, which prevents MQ from starting entirely. You just need to turn off LFQ.

Indeed, it crashes on Windows too with only one sample. I tried again with 2 samples on Windows, works fine.

So I tried again on Linux. This time, I filled all the columns in the Raw data panel, and made sure to include 2 samples. It is now running in Linux.

However, it appears to be stuck at "MS/MS first search". Will let it run for one more day, will update.

Thank you.

[WalterViegener]

Hi,
Can you please send me some example data here? we will try to take a look

Best,
Walter

[gitMakeCoffee]

Hello,

I'm very sorry for the delay.
I have uploaded 3 raw files to the link you provided.
Please let me know what you think.
Thanks again for your time and help.