Understanding ValueError error messages

The full error is usually a longer message seen only after clicking on the bug icon or by reviewing the job details stderr.

How to do both is covered in the Troubleshooting errors FAQ.

Many lines of text, may include parameters
ValueError: invalid literal for int() with base 10: some-sequence-read-name
  • Causes:
    • MACS2 produces this error the first time it is run. MACS is not the only tool that can produce this issue, but it is the most common.
  • Solutions:
    • Try at least one rerun.
    • MACS/2 is not capable of interpreting sequence read names with spaces included. Try following these two:
      • Remove unmapped reads from the SAM dataset. There are several filtering tools in the groups SAMTools and Picard that can do this.
      • Convert the SAM input to BAM format with the tool SAMtools: SAM-to-BAM. When compressed input is given to MACS, the spaces are no longer an issue.
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