Albacore basecalling all files each loop

[clarepacini]

Hi,

Thanks for the scripts, they have been very useful so far! I have one (possibly silly) question. I am running the following script:

#!/bin/bash while true; do rm -rf /mnt/home1/gurdon/cep46/MinionSeq/staging2;

python stageflowcells.py /mnt/home1/gurdon/cep46/MinionSeq/data/reads/$2 /mnt/home1/gurdon/cep46/MinionSeq/basecalls /mnt/home1/gurdon/cep46/MinionSeq/staging2

read_fast5_basecaller.py -r -i /mnt/home1/gurdon/cep46/MinionSeq/staging2/$1 -s /mnt/home1/gurdon/cep46/MinionSeq/basecalls/$1 -t 10 -f FLO-MIN106 -k SQK-LSK108 $3 sleep 10 ; done

$1 is the flowcell, for $2 I am passing the name of the experiment folder, and $3 are any other options to albacore. But on each iteration, albacore is re-basecalling all reads. Am I passing the incorrect directories to the staging script?

Thanks,

Clare