Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Error in CollectGcBiasMetrics during ATAQC module

See original GitHub issue


I am running the pipeline starting with nodup.bam files. The pipeline seemed to run successfully with previous version of the pipeline. However, when I downloaded the latest version of the pipeline couple of days ago, the pipeline breaks at picard’s CollectGcBiasMetrics command during ATAQC module with Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 130695116 out of bounds for length 130694994 error. After some investigation, I found where the out of bounds numbers are coming from. The length of chr10 is 130694993 and there is a read that maps to chr2 at 130695116. What is not clear is why picard tries to use length of chr10 for read mapping to chr2. I did little more investigation to find out the scripts that are calling picard’s CollectGcBiasMetrics. It looks like before the get_gc function, which runs CollectGcBiasMetrics, is called by, the input bam file is processed to remove read groups. However, this feature seem to be missing in older version of I am not sure if this is the culprit or I am doing something wrong. Please advice.

Thank you for your time.


Issue Analytics

  • State:closed
  • Created 4 years ago
  • Comments:7 (3 by maintainers)

github_iconTop GitHub Comments

leepc12commented, Apr 17, 2019

Yes, you can keep using the TSV file mm10.tsv. In your input JSON file, define the following to override reference FASTA defined in the TSV file.

    "atac.ref_fa" : "PATH_FOR_YOUR_OWN_FASTA"
ravipatel4commented, Apr 18, 2019

That worked! Thanks @leepc12 and @vervacity.

Read more comments on GitHub >

github_iconTop Results From Across the Web

Error in running CollectGcBiasMetrics - GATK
Hi I am trying to run CollectGcBiasMetrics on my sorteed bam file: my command is : java -Xms4096m -jar build/libs/picard.jar...
Read more >
ataqc/ at master - GitHub
Script to run ataqc, all parts. import matplotlib. matplotlib.use('Agg'). import os. import sys. import pysam. import pybedtools. import metaseq.
Read more >
Tool documentation - GitHub Pages
This 'meta-metrics' tool runs one or more of the metrics collection modules at the same time to cut down on the time spent...
Read more >
Usage - atacseq » nf-core
The sample identifier is the same when you have multiple biological replicates from ... the file we want is modules/nf-core/software/star/align/ .
Read more >
Run picard CollectGcBiasMetrics to generate QC metrics pertaining to GC bias. ... used to request RAM during cluster job submission as `{resources.mem_mb}`: ...
Read more >

github_iconTop Related Medium Post

No results found

github_iconTop Related StackOverflow Question

No results found

github_iconTroubleshoot Live Code

Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free

github_iconTop Related Reddit Thread

No results found

github_iconTop Related Hackernoon Post

No results found

github_iconTop Related Tweet

No results found

github_iconTop Related Post

No results found

github_iconTop Related Hashnode Post

No results found