Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[MaxQuantCmd 2.4.12.0] crosslinking search error "peptides.ind not found" #53

Open
COCOJJLEE opened this issue Dec 27, 2023 · 0 comments

Comments

@COCOJJLEE
Copy link

Describe the bug
Searching for MS/MS cross-linking,
The file "/storage/maxquant/both_substitution/combined/clsearch/pep/peptides.ind" was not found."" with the error

To Reproduce
Steps to reproduce the behavior:
1. within the maxqaunt GUI application on a Window operating system, define and save a new crosslinking. (See figure 1)
2. Copy the entire Maxquant 2.4.12.0 directory and move it to a Linux virtual server.
3. modify the mqpar.xml file created on Windows to suit the Linux system.
4. Create a mono environment with the Mono JIT compiler version 6.12.0.90 using conda (
conda create -n mono, conda install mono)
5. submit a job to slurm
#!/bin/bash
#SBATCH -J Maxquant
#SBATCH -t UNLIMITED
#SBATCH -p Node1
#SBATCH -n 42
mono /home/program/MaxQuant_v_2.4.12.0/MaxQuant_v_2.4.12.0/bin/MaxQuantCmd.exe mqpar.xml
6. although all previous steps are successful,
MS/MS crosslink search step
error "System.IO.FileNotFoundException: Could not find file "/storage/maxquant/both_substitution/combined/clsearch/pep/peptides.ind"".

Expected behavior

Screenshots
If applicable, add screenshots to help explain your problem.

maxquant_crosslinking_error_1

Desktop (please complete the following information):

  • OS: CentOS Linux release 7.9.2009
  • Version MaxQuantCmd 2.4.12.0

Additional context
If the composition of the hydrolyzed composition and the linked composition are exactly the same, the program will run without errors.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant