Understanding ValueError error messages

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• /faqs/galaxy/analysis_job_failure_value_error title: Understanding ValueError error messages area: troubleshooting box_type: tip layout: faq contributors: [jennaj, garimavs] —

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.

stderr
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Many lines of text, may include parameters
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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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