Repeat mask short read genomes using the same library for the reference genome. Convert hard masking to soft masking.
sbatch SRrepeat.sh
sbatch hardtosoft.sh
Transfer hardmasked files to kubernetes
rclone mkdir steps-output
rclone copy . nrp1:steps-output --include "*-hardmasked.fa"
Prepare the split file to run parralellization of cactus
/home/cactus/cactus_env/bin/cactus-prepare pseudlocal.txt --outDir steps-output --outSeqFile steps-output/pseud.txt --outHal steps-output/pseud.hal --jobStore jobstore_steps --gpu 1
Split each set into a file named after the ancestor it creates, name the file something like f05.txt (whatever the ancestor is)
Make a file round0.txt with the list of parralel processes in the round to run. Then submit all jobs:
while IFS= read -r name; do
echo $name
template=stepspseud.yml
sed "s/ANC/$name/g" ${template} > temp_${name}.yml
rclone copy ${name}.txt nrp1:config
kubectl delete -f temp_${name}.yml
kubectl create -f temp_${name}.yml
#kubectl delete -f temp_${name}.yml
done < round0.txt
"error: error validating "preppseud.yml": error validating data: failed to download openapi: Get "https://67.58.53.147:6443/openapi/v2?timeout=32s": failed to refresh token: oauth2: cannot fetch token: 401 Unauthorized Response: error="invalid_token" error_description="token+not+found"" Renew key by going to https://portal.nrp.ai/ and clicking 'get config'. switch the ~/.kube/config file with the new file that downloaded.