bcftools annotate max outsize is 300G
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 30/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start by reproducing the two reported bcftools annotate commands with the affected input and annotation files, then trace the repeated [E::bgzf_flush] hwrite error. Done means annotate completes without producing an unexpectedly oversized output file or write errors for the reported operations.
Written by the indexing model from the issue text.
Description
Hi there,
Every time I run bcftools annotate on one of my files (which produces a file > 300GB), it fails and makes a file of size >15TB. Error:
Both -a/-c and -x fail:
bcftools annotate -a file.anno -c INFO file.in -Ob -o file.out
bcftools annotate -x 'INFO/ID' file.in -Oz -o file,out
Errors look like this:
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
[E::bgzf_flush] hwrite error (wrong size)
Best wishes,
Chris
- Dominant language
- C
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- Merged PRs (30d)
- 2
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