Offload fastq data from the Ion Torrent at MGL

Offload_fastq_data_Ion_Torrent.md

Offload fastq data from the Ion Torrent at MGL

How to obtain fastq data from the Ion Torrent server at MGL. Requires that the plugin FileExporter has been run.

1. Mount USB on system

Plug in the USB drive into the system.
Use sudo fdisk -l to find where your drive is mounted.
Mount via: sudo mount /dev/sde1 /media/<your_drive> (where /dev/sde1 is the location of drive found above, your_media is your drive name).

2. Find the output files

If data is still on the system drive, the plugin results are here:
/results/analysis/output/Home/<your_run>/plugin_out/FileExporter_XXX (where XXX is a number of your FileExporter run)

If data has been archived, the plugin results are here:
/mnt/nas-volumes-pool-share1/archivedReports/<your_run>/plugin_out/FileExporter_out.XXXX/

3. Compress the output files

Note: this will compress with gzip, but will delete the uncompressed files.
If the files are in the archive, just move them without compressing.

# Compress
gzip *.fastq     
# Calculate md5
md5sum *.fastq.gz > <your_run.md5>

4. Make output directory on the external drive and copy results

mkdir /media/<your_drive>/raw_data/<species>/<run_name> # Note: run_name is the same as your md5 name
# Move out of FileExporter folder
cd ..
rsync -avzP ./FileExporter_out.XXXX /media/<your_drive>/raw_data/<species>/<run_name>` # Note: XXXX is the FileExporter number

5. Unmount

sudo umount /media/<your_drive>

6. Move drive onto target computer

Use rsync as above to move the data onto your target computer, then make sure to check your md5 checksums:
md5sum -c /<your>/<target>/<file>/<structure>/*.md5

7. Analyze away!