How to keep the alignment?

[FranckLejzerowicz]

Hello,

In this ReadTheDocs page, it is shown in the anatomy of the per-sample run_snps outputs, that the alignments are present:

|- temp
     |- snps
        |- repgenomes.bam              run_snps        Rep-genome alignment file
        |- {species}/snps_XX.tsv.lz4
  |- bt2_indexes
     |- snps/repgenomes.*              run_snps        Sample-specific rep-genome database

However, both the temp and bt_indexes folder turn out empty after a successful run of run_snps.

I do not remove these files and I do see in the stdout:

• lines such as:

  1695133677.6:  'samtools index -@ 4 /<my_path>/temp/snps/111210/111210.sorted.bam'

  but this file is nowhere to be found after completion.

I consider hacking the tool for not-removing these files that would be useful to my work.

Please, is there a way/flag to tell midas2 to keep these output files?

Thanks, Franck

[FranckLejzerowicz]

Probably answering to myself here, but the code seems to allow for --debug to get me where I want - correct? https://github.com/czbiohub-sf/MIDAS2/blob/a293ce62355e88dc0f12145871ff47110bc8f712/midas2/subcommands/run_snps.py#L850-L853 Thanks

[zhaoc1]

Yes! --debug is the way to go for keeping all the temp files, including the alignment files.