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Augmentation failed on one chromosome, but succesfull on other chromosomes #4283
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Looks like maybe the gam file is nonexistent or corrupted. You can verify by doing something like
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It reports similar messages. How to chunk the gam only for chr 17? I chunk the vg and gam together before.
the pg is valid
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I think you have to hcunk the vg and gam together (depsite what the options may lead you to believe). You can just do that and only use the gam output. |
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1. What were you trying to do?
I tried to call vcf for each splitted chromosome after aligning short reads against the variation graph.
2. What did you want to happen?
Vcfs for all chromosome should be called separately.
3. What actually happened?
One chromosome reported error on the agumentation step while vcfs for other chromosomes were successfully called.
4. If you got a line like
Stack trace path: /somewhere/on/your/computer/stacktrace.txt
, please copy-paste the contents of that file here:5. What data and command can the vg dev team use to make the problem happen?
These are the subsequent steps I executed. For this chr17, it failed on the augmentation step.
6. What does running
vg version
say?The text was updated successfully, but these errors were encountered: