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mbhall88 / drprg

Drug Resistance Prediction with Reference Graphs
https://mbh.sh/drprg/
MIT License
19 stars 1 forks source link

Index is not valid, missing files error #39

Closed belarus1941 closed 3 months ago

belarus1941 commented 3 months ago

Dear Developers, I am trying to use and run your software, however nothing helps to fix the errors, which appear:

#!/bin/bash 

sudo docker run --rm=True -v $PWD:/home/mat29/indata/ -u $(id -u):$(id -g) staphb/drprg drprg index --download  -o/home/mat29/indata/   

sudo docker run --rm=True -v $PWD:/home/mat29/indata/ -u $(id -u):$(id -g) staphb/drprg drprg predict -x/home/mat29/indata/mtb -i/home/mat29/indata/reads.fastq  --illumina -o/home/mat29/indata/ 

System shows:

#[2024-03-27T17:25:47Z INFO ] mtb index version 20230308 already downloaded. Skipping...
#[2024-03-27T17:25:47Z INFO ] Done!
#Error: Index is not valid due to missing file "/home/mat29/indata/mtb/dr.prg.kX.wY.idx"

If I create the new file dr.prg.kX.wY.idx, system throws the other similar error that there is another file missing. And it never ends I need to run your software on the M. Tuberculosis FASTQ Illumina genomic files.

Please advise what Shell code to run and what to change, how to fix the problem? Thank you.

Dr. Matvey

mbhall88 commented 3 months ago

When you specify a different path to download the index to, you need to use the explicit path to the index you want when predicting. So your predict command should be

sudo docker run --rm=True -v $PWD:/home/mat29/indata/ -u $(id -u):$(id -g) staphb/drprg drprg predict -x/home/mat29/indata/mtb/mtb-20230308 -i/home/mat29/indata/reads.fastq  --illumina -o/home/mat29/indata/
belarus1941 commented 3 months ago

thank you, it works...