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YCGA Sequence Data Archive

Retrieve Data from the Archive

In the sequencing archive on Ruddle, a directory exists for each run, holding one or more tar files. There is a main tar file, plus a tar file for each project directory. Most users only need the project tar file corresponding to their data.

Although the archive actually exists on tape or in cloud storage, you can treat it as a regular directory tree. Many operations such as ls, cd, etc. are very fast, since directory structures and file metadata are on a disk cache. However, when you actually read the contents of files the file is retrieved and read into a disk cache. This can take some time.

Archived runs are stored in the following locations.

Original location Archive location
/panfs/sequencers /SAY/archive/YCGA-729009-YCGA-A2/archive/panfs/sequencers
/ycga-ba/ba_sequencers /SAY/archive/YCGA-729009-YCGA-A2/archive/ycga-ba/ba_sequencers
/gpfs/ycga/sequencers/illumina/sequencers /SAY/archive/YCGA-729009-YCGA-A2/archive/ycga-gpfs/sequencers/illumina/sequencers

You can directly copy or untar the project tarfile into a scratch directory.

Info

Very large tar files over 500GB, sometimes fail to download. If you run into problems, contact us at hpc@yale.edu and we can manually download it.

cd ~/scratch60/somedir
tar –xvf /SAY/archive/YCGA-729009-YCGA-A2/archive/path/to/file.tar

Inside the project tar files are the fastq files, which have been compressed using quip. If your pipeline cannot read quip files directly, you will need to uncompress them before using them.

module load Quip
quip –d M20_ACAGTG_L008_R1_009.fastq.qp

For your convenience, we have a tool, restore, that will download a tar file, untar it, and uncompress all quip files.

module load ycga-public
restore –t /SAY/archive/YCGA-729009-YCGA/archive/path/to/file.tar

If you have trouble locating your files, you can use the utility locateRun, using any substring of the original run name. locateRun is in the same module as restore.

locateRun C9374AN

Restore spends most of the time running quip. You can parallelize and thereby speed up that process using the -n flag.

restore –n 20 ...

Tip

When retrieving data, run untar/unquip as a job on a compute node, not a login node and make sure to allocate sufficient resources to your job, e.g. –c 20 --mem=100G.

Tip

The ycgaFastq tool can also be used to recover archived data. See here.

Example:

Imagine that user rdb9 wants to restore data from run BHJWZZBCX3

step 1

Initialize compute node with 20 cores

salloc -c 20
module load ycga-public

step 2

Find the run location

$ locateRun BHJWZZBCX3
/ycga-gpfs/sequencers/illumina/sequencerV/runs/210305_D00306_1337_BHJWZZBCX3.deleted
/SAY/archive/YCGA-729009-YCGA-A2/archive/ycga-gpfs/sequencers/illumina/sequencerV/runs/210305_D00306_1337_BHJWZZBCX3

Note that the original run location has been deleted, but the archive location is listed.

step 3

List the contents of the archived run, and locate the desired project tarball:

$ ls -1 /SAY/archive/YCGA-729009-YCGA-A2/archive/ycga-gpfs/sequencers/illumina/sequencerV/runs/210305_D00306_1337_BHJWZZBCX3
210305_D00306_1337_BHJWZZBCX3_0.tar
210305_D00306_1337_BHJWZZBCX3_0_Unaligned_Project_Jdm222.tar
210305_D00306_1337_BHJWZZBCX3_1_Unaligned-1_Project_Rdb9.tar
210305_D00306_1337_BHJWZZBCX3_2021_05_09_04:00:36_archive.log

We want 210305_D00306_1337_BHJWZZBCX3_1_Unaligned-1_Project_Rdb9.tar, matching our netid.

step 4

Use the restore utility to copy and uncompress the fastq files from the tar file. By default, restore will start 20 threads, which matches our srun above. The restore will likely take several minutes. To see progress, you can use the -v flag.

restore -v -t /SAY/archive/YCGA-729009-YCGA-A2/archive/ycga-gpfs/sequencers/illumina/sequencerV/runs/210305_D00306_1337_BHJWZZBCX3/210305_D00306_1337_BHJWKHBCX3_1_Unaligned-1_Project_Rdb9.tar

The restored fastq files will written to a directory like this:

210305_D00306_1337_BHJWZZBCX3/Data/Intensities/BaseCalls/Unaligned*/Project_*


Last update: September 9, 2022