Fri. Jul. 19, 2019 Salmon sea lice methylomes

Received salmon sea lice methylome data!!

copy data to Gannet metacarcinus folder

  • I received this url from the sequencing core
  • I mounted gannet via finder -> connect to server
  • I installed Globus Connect Personal on Ostrich and gave the Globus app writing permissions to my metacarcinus folder on Gannet
  • I navigated to my Globus account file manager section via the provided url and could see my sequencing data “UW_Trigg_190718.tar.gz” 148.22GB.
  • I selected the “Transfer of Sync to…” option, entered the computer name “Ostrich” which I entered when setting up Globus Connect Personal app, entered the path “/Volumes/web/metacarcinus/Salmo_Calig/FASTQS/”. Then clicked start. img
  • I navigated to the Activity section of Globus and could see the info being transferred (26GB in 10min) img
  • after a couple hours, I received an email notification and could see in the status section that the transfer had completed successfully img

copy data from Gannet to mox

ran this command:

rsync --archive --progress --verbose strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718.tar.gz /gscratch/srlab/strigg/data/Salmo_Calig/FASTQS/

I decided to make two species folders rather than have them combined, and wanted to remove the data that was not Salmon or sea lice fastqs, so ran the following commands:

tar -xvf UW_Trigg_190718.tar.gz
cd UW_Trigg_190718_done/
rm -r Reports/
rm -r Stats/
rm -r Undetermined_S0_L00*
cd ../../../
mkdir Caligus
mv Salmo_Calig/ Ssalar
cd Ssalar/
cd FASTQS/
cd ..
cd Caligus/
mkdir FASTQS
mv ../Ssalar/FASTQS/UW_Trigg_190718_done/Sealice_F* .
mv *.gz FASTQS/
rm UW_Trigg_190718.tar.gz 

copy data from Gannet to owl

run fastqc and trim

  • prepared scripts (Salmon: /gscratch/srlab/strigg/jobs/20190719_FASTQC_ADPTRIM_Ssalar.sh and lice: /gscratch/srlab/strigg/jobs/20190719_FASTQC_ADPTRIM_Caligus.sh) to do this on Mox but didn’t work because multiqc and cutadapt programs could not be found as I had them. See github issue #712
Written on July 19, 2019