Software⏱️ 3 min read📅 2026-06-11

How to Fix Error code 140 Error – Error code 140 in command running through Nextflow on SLURM

Error code 140 in Nextflow script on SLURM cluster, tr command failure.

Quick Answer: Check the output of the command to see if there are any error messages that might indicate what's causing the issue.

📋 Table of Contents

  1. 🔍 Why This Happens
  2. 🔧 Proven Troubleshooting Steps
  3. 💡 Conclusion

Error code 140 in command running through Nextflow on SLURM is a frustrating issue that affects users who are trying to debug commands that fail with this specific exit status. This error can be caused by various factors, including incorrect usage of the tr command or issues with the underlying system configuration.

The lack of detailed information about the cause of this error makes it challenging for users to identify and resolve the issue. However, by following the steps outlined in this guide, you should be able to diagnose and fix the problem.

🔍 Why This Happens

  • One main reason why Error code 140 occurs is due to incorrect usage of the tr command. The tr command expects two file descriptors as arguments, but it seems that only one file descriptor is being provided in the Nextflow script. This can be fixed by modifying the script to include both file descriptors.
  • Another possible cause of this error is related to the SLURM scheduler configuration. It's possible that the SLURM scheduler is not properly configured or is experiencing issues, which could lead to the tr command failing with exit code 140.

🔧 Proven Troubleshooting Steps

Correcting the tr command usage

  1. Step 1: Open the Nextflow script and locate the line containing the tr command. Ensure that both file descriptors are being provided as arguments.
  2. Step 2: Modify the script to include both file descriptors, like this: cat in_file | tr -d ' ' -f out_file > out_file
  3. Step 3: Save the changes and re-run the Nextflow script to test if the error is resolved.

Checking SLURM scheduler configuration

  1. Step 1: Check the SLURM scheduler configuration files (usually located in /etc/slurm.conf or /etc/schedconf.d/) for any errors or inconsistencies.
  2. Step 2: Verify that the SLURM scheduler is properly configured and running correctly. You can do this by checking the slurmctld logs for any error messages.
  3. Step 3: If necessary, modify the SLURM configuration files to resolve any issues and restart the slurmctld service.

💡 Conclusion

In conclusion, Error code 140 in command running through Nextflow on SLURM can be caused by incorrect usage of the tr command or issues with the underlying system configuration. By following the steps outlined in this guide, you should be able to diagnose and fix the problem. Remember to always double-check your script and configuration files for any errors or inconsistencies.

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