# FreeBayes regd.

**URL:** <https://help.galaxyproject.org/t/freebayes-regd/12003>\
**Category:** Uncategorized\
**Tags:** devops-administration, galaxy-local, variant-analysis\
**Created:** [March 24, 2024, 12:04pm UTC](https://help.galaxyproject.org/t/freebayes-regd/12003 "2024-03-24T12:04:21Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![susheel\_raina](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/susheel_raina/32/2052_2.png) [@susheel\_raina](https://help.galaxyproject.org/u/susheel_raina)\
**Post date:** [March 24, 2024, 12:04pm UTC](https://help.galaxyproject.org/t/freebayes-regd/12003/1 "2024-03-24T12:04:21Z")

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Hi,

I followed a FASTQC-BWA-MEM-Samtools view-RmDup-FreeBayes pipeline.  
Everything was working fine upto RmDup. However, after having executed  
FreeBayes tool, the results reveal 0 lines with comments as below:  
[W::hts\_idx\_load3] The index file is older than the data file: b\_71.bam.bai  
[W::hts\_idx\_load3] The index file is older than the data file: b\_60.bam.bai  
[W::hts\_idx\_load3] The index file is older than the data file: b\_19.bam.bai  
[W::hts\_idx\_load3] The ind

Please help.

regards  
Susheel

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [March 25, 2024, 11:35pm UTC](https://help.galaxyproject.org/t/freebayes-regd/12003/2 "2024-03-25T23:35:49Z")

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Hi @susheel_raina

Lines like this are general warning logs from the tool that can be ignored when troubleshooting:

> [@susheel\_raina](#):
>
> [W::hts\_idx\_load3] The index file is older than the data file: b\_71.bam.bai

If you are not getting any results, what to check

1. Does the BAM still contain mapped reads? Samtools stats is one tool choice.
2. Will those mapped reads will pass the filtering criteria set on the tool form? Click into the “i” icon’s job info page to review all applied parameters in a plainer text format.
3. Re-confirm that the BAM’s reference index is based on the same genome assembly as chosen on the tool form. Remember this must be exact: even down to the specific way the chromosomes are named.
4. Learn at GTN → [Tutorials using Freebayes](https://training.galaxyproject.org/training-material/by-tool/devteam/freebayes.html)

If all that checks out, you can share back your work for more troubleshooting here. This will need the job details, a peek at the file content and metadata plus the server you are working at. Please see the banner at this forum, or directly here, for the how-to →

- [Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/docs?topic=42)
- [How to get faster help with your question](https://help.galaxyproject.org/docs?topic=11469)

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [March 17, 2026, 4:43am UTC](https://help.galaxyproject.org/t/freebayes-regd/12003/3 "2026-03-17T04:43:56Z")

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Closed on March 17, 2026, 4:43am UTC