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WGLab / NanoCaller

Variant calling tool for long-read sequencing data
MIT License
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index file .fai error #25

Open Meirom-Michal opened 2 years ago

Meirom-Michal commented 2 years ago

Hello, While trying to run NanoCaller_WGS

I receive the error-index file .fai required for reference genome file, although the index file exists in the same folder as the ref genome. What could be the reason?

Thanks

umahsn commented 2 years ago

Hi Meirom,

Can you check the error output and let me know what is the exact error message, or if this error is coming from pysam?

I have released a new version of NanoCaller which does not use .fai file to get names of reference contigs, and instead gets them from BAM file instead. If that is where the error is coming from then it should be solved in the new version, but if there is some other source for this, perhaps from pysam opening reference file then I can look into that as well. Also, in the new version there is no NanoCaller_WGS, you can use just NanoCaller command.

Meirom-Michal commented 2 years ago

This is the error message:

2022-06-08 19:26:27.514511: Starting NanoCaller. NanoCaller command and arguments are saved in the following file: /home/ps/test_nanocaller/args 2022-06-08 19:26:27.514539: index file .fai required for reference genome file. No files are generated in the output folder.

I will also try the new version.

Thanks