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cgpu/storage_30x.md

Last active February 2, 2020 13:19
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storage_30x.md 
[ec2-user@ip-172-31-29-73 ~]$ df -h 
Filesystem      Size  Used Avail Use% Mounted on
devtmpfs        121G   68K  121G   1% /dev
tmpfs           121G     0  121G   0% /dev/shm
/dev/xvda1      5.3T  682G  4.7T  13% /
sudo nextflow run https://github.com/PGP-UK/GenomeChronicler-Sarek-nf \
--input 's3://lifebit-featured-datasets/pipelines/genomechronicler/PGPUK__uk35C650.tsv' \
--genome GRCh38 \
--step Mapping \
--tools 'HaplotypeCaller,VEP,GenomeChronicler' \
--monochrome_logs \
--max_cpus 32 \
--max_memory '240.GB' \
--noGVCF \
--skipQC all \
-with-trace /home/ec2-user/nf-out/trace.txt \
-process.cache lenient \
-resume \
-profile docker
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