Comments (3)
@rarsenal Thanks for bringing this to our attention. I will try to reproduce this. What version of python are you running?
Also, did any errors occur when building the reference genome fasta? This issue seems like it could be related to #64 but that only occurred with a custom fasta file.
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Hi jjzieve,
Thanks for the fast reply! Actually I just found the source of the error. I containerized the various tools for the pipeline we are building, so the container had both python2 and python3 environments built in. After I separated the GTCtoVCF component into a standalone container with only miniconda2 base environment, everything is working as expect. I suppose that GTCtoVCF was inadvertently running on python3 and while it produced no runtime errors, its bytes/string decoding functions are not compatible with python3? Anyhow, thanks again for your attention, and you can close the issue when you see fit.
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Glad you found the issue! In hindsight, should've known the byte vs. string issue would be a python2 vs. 3 underlying cause.
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Related Issues (20)
- GTC converter - WARNING - Reference is missing entry for chromosomes HOT 8
- Precision difference when updating numpy versions
- GTC parser error : All GT values in converted vcf are './.' HOT 4
- Illumina Generated Manifest has no RefStrand column HOT 5
- Replace ID in output VCF with `--id` option
- GQ type is "String" instead of "Float" HOT 1
- download_reference.sh is outdated HOT 3
- Unable to run download_reference.sh on Mac HOT 3
- Unclear Error message HOT 1
- Next release HOT 2
- download_reference script has broken links HOT 2
- Reference not detected if lowercase characters HOT 4
- Python3 Question HOT 3
- SourceSeq validation failures should be skipped instead of erroring out
- Bus error when converting GTC to VCF HOT 7
- GQ score clarification HOT 3
- Python3 support HOT 1
- ERROR - Reference is missing entry for chromosome 3 HOT 2
- Any experience about GQ settings HOT 1
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