MaxQuant troubleshooting

1

Dear Lati98,
How did you resolve this issue? Would you please share your solution?
I have the same problem and my input data format (thermo.raw) and integrity looks good, as it should be, no input file or file name duplicates etc.
Thank you in advance for your help.
Best regrds.
(Qc)

2

Hi @qcsciphi

There wasn’t any followup and your problem is likely different.

That specific message about duplicate inputs is just an automated guess. If the tool cannot read the inputs, that message can be triggered, too or one of these extra alternative messages Galaxy Training! (varies by server if reported or not).

Short advice:

  1. Make sure that the reads are in an uncompressed state and assigned the datatype: fasta
  2. Then review the regular expressions that are parsing the read name and description content (what is on the > title lines). The default will not work for every file, and if not a match for your specific reads could certainly result in a “duplicate read name”.
  3. There are two different versions of this tool. One requires just a fasta and the other a thermo.raw + fasta input + mqpar.xml.
  • The tool must be able to match identifiers across all user supplied inputs plus any values parsed out of them at runtime.

mqpar.xml file with your search parameters. RAW file names must match the names displayed in galaxy. Their paths from the local machine are ignored. E.g. a file named ‘test01.raw’ in galaxy can either be named ‘test01.raw’ or ‘D:\path\to\test01.raw’ in the mqpar.xml. * required

For more help, please copy the inputs into a new history, then attempt to run the tool. If it still fails and you cannot figure out how to fix the regular expressions, please do one of these:

  • generate and post back a shared link to that small testing history (probably required if the input is more than a single fasta)
  • or, post back to this topic:
    a. the first few sequences in full – at least three reads
    b. the regular expressions in use – will be at least two: identifier + description
    c. the tool full name including version (copied from the very top of the tool form)
    d. a copy + paste of the “Dataset Details” view, all parts from the “Tool Parameters” portion and down should be enough to start with. Find this by clicking on the :information_source: icon within one of the output datasets faqs/galaxy/#troubleshooting-errors

Let’s start there, thank you :slight_smile:

3

Hi JennaJ,
Thank you for your kind suggestions.
We are talking about the GTN training material: “MaxQuant and MSstats for the analysis of TMT data”;

When you click on the “graduation hat” icon on Galaxy.eu and search for “MaxQuant and MSstats for the analysis of TMT data” training material now there’s a message appearing, which says;

" Under Development!
This tutorial is not in its final state. The content may change a lot in the next months. Because of this status, it is also not listed in the topic pages."

Probably the specialists are checking the steps that you’re suggesting.
Thank you once again for your kind assistance.

Regards,
Qc

1 Like