No sequences in core_genome_alignment.aln

[wanyuac]

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]

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]

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