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seppinho / haplogrep-cmd

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
https://haplogrep.i-med.ac.at/
MIT License
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Remove jbwa-xxxx folder after running HaploGrep #33

Closed alexhbnr closed 4 years ago

alexhbnr commented 4 years ago

Hello,

After running HaploGrep2 on a Linux server using a FastA file as an input, HaploGrep2 successfully generates the HSD report file, but does not clean up the empty jbwa-xxxx folder. If I run HaploGrep2 on a larger number of files, I have hundreds of empty folders at the location from which HaploGrep2 was called.

Here is the command I am using: java -Xms256m -Xmx1G -jar haplogrep-2.1.25.jar --in ${input} --extend-report --format fasta --hits 5 --out ${output}

Is this behaviour on purpose or could HaploGrep2 remove this folder automatically before shutting itself down?

seppinho commented 4 years ago

thanks. I will provide a fix. sorry for that! How does the fasta converter work? Would be great if you have some eval results for us.

alexhbnr commented 4 years ago

The FastA converter works well, as far as I am aware. I used it on > 3,500 samples as part of a pipeline and it did not crash or give weird errors. However, I did not check whether I get the same results when using a different input format. Should I be concerned when using it?

seppinho commented 4 years ago

FASTA test cases looking good, I was just curious :) Regarding the reported issue: I checked the source and the jbwa directory should be deleted. It gets deleted on my Linux, did not change this for a while. Can you please double check using the latest version (see Readme). Thanks!

alexhbnr commented 4 years ago

Thanks, @seppinho, I tested the latest release (v2.2.5) and it works now fine.