bacpop / ggCaller

Bifrost graph gene caller.
MIT License
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No sequences in core_genome_alignment.aln #12

Closed wanyuac closed 11 months ago

wanyuac commented 11 months ago

Hi Sam,

Thanks for developing ggCaller and it is wonderful. Recently, I used ggCaller v1.3.4 on my Ubuntu 22.04.3 LTS system to generate a pangenome graph for 73 bacterial genomes with the following command:

docker run -it -v $(pwd):/workdir samhorsfield96/ggcaller:latest ggcaller --refs inputs.txt --clean-mode sensitive --annotation ultrasensitive --alignment pan --core-threshold 1.0 --threads 32 --save --out ggcaller_output_pan100 --quiet

The output core-gene alignment core_genome_alignment.aln only had sequence headers, which was not the case when --alignment core:

docker run -it -v $(pwd):/workdir samhorsfield96/ggcaller:latest ggcaller --refs inputs.txt --clean-mode sensitive --annotation ultrasensitive --alignment core --core-threshold 1.0 --threads 32 --save --out ggcaller_output_core100

I have attached the output file from the first command for your information. I would be much grateful if you would help me to investigate this problem. core_genome_alignment.aln.zip

samhorsfield96 commented 11 months ago

Hi Yu, thank you! Sorry to hear you're having trouble. I've fixed this issue in commit 4fc76f2, please let me know if you have any further problems.

wanyuac commented 11 months ago

Hi Sam, thank you very much for solving this issue!