Transferred data from conference room computer (genefish) to Owl. See post for details.

Downloaded from Azenta

I originally downloaded the data from Azenta via CyberDuck (See post: MUSP RNAseq Data Received), and then I left for a writing retreat with Melanie and Alyssa to Quadra Island, BC, Canada!

Check md5 before transferring to OWL

md5 checksums are unique number codes that are used to confirm the integrity of files after downloading. I followed what we did in this GitHub Issue: 1460. There’s a lot of information in there, so here’s exactly what needs to be done:

On genefish, open terminal and navigate to the folder where the data lives.

Then run:

for checksum_file in *.md5
do
# Gets filename without any suffixes
filename=$(basename -s .fastq.gz.md5 ${checksum_file})
# Generates MD5 checksum and compares to provided checksum in MD5 file
diff <(md5 "${filename}.fastq.gz" | awk '{print $4}') <(awk '{print $1}' ${checksum_file})
done

This will take some time, so go and do something else and come back!

Checked at 4:45pm and it showed no errors, so all is good!

Now I’m rsync-ing the files to Owl:

rsync --archive --progress --verbose PSC*.fastq.gz grace@128.95.149.83:/volume1/web/nightingales/P_helianthoides/

Check md5 checksums after rsync-ing to OWL

Confirm that it all went well. Navigate in command line to the grace@Owl:/var/services/web/nightingales/P_helianthoides directory and run:

for fastq in PSC*.fastq.gz
do
  md5sum "${fastq}" >> checksums.md5
  echo "Generated checksum for ${file}."
  echo ""
done

when complete, run:

cat checksum.md5

and the new libraries for multispecies are in the file! all good!