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mbhall88 / tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
MIT License
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Directory input bug #17

Closed leoisl closed 2 years ago

leoisl commented 2 years ago

I have the following directory structure: sample_example/mada_101/mada_101.nanopore.fastq.gz. If I run tbpore giving the sample_example dir as input, I get this issue:

(tbpore) leandro@leandro-ThinkPad-X1-Carbon-6th:~/git/tbpore$ poetry run tbpore sample_example
[2022-04-26 10:36:34] INFO     | Welcome to TBpore version 0.1.0
[2022-04-26 10:36:34] INFO     | Searching for fastq files...
[2022-04-26 10:36:34] INFO     | Found 0 fastq files. Joining them...

And it gets stuck here

leoisl commented 2 years ago

Fixed in https://github.com/leoisl/tbpore/commit/766dc8bd620e02e56cd96a7625cb7cd64bbd271f . Now we get this:

(tbpore) leandro@leandro-ThinkPad-X1-Carbon-6th:~/git/tbpore$ poetry run tbpore sample_example
[2022-04-26 10:55:21] INFO     | Welcome to TBpore version 0.1.0
[2022-04-26 10:55:21] INFO     | Searching for fastq files...
[2022-04-26 10:55:21] ERROR    | No fastq files found for the given inputs, please check your input files/dirs.
[2022-04-26 10:55:21] ERROR    | Tip: to search for fastq files recursively, please use the --recursive flag.
mbhall88 commented 2 years ago

Excellent logging