SRAToolkit - Delete cache after each sam-dump run
1
0
Entering edit mode
3.7 years ago

Hi everyone ,

I'm trying to do a bunch of sam-dumps (piping the .sam outputs to .bam) - however, each time sam-dump runs, a sizeable cache file gets created in the sra directory. Since I need to run sam dumps around 4000 times, I can't possibly keep the caches anywhere because it'll be a few terabytes large. So, I need to delete them as soon as I'm done with each sam-dump. How can I achieve this in a shell script?

I tried running cache-mgr -c, but it ends up clearing out the .bam files I need to keep as well.

Thanks!

sequence sra sratoolkit sam-dump • 1.8k views
ADD COMMENT
2
Entering edit mode
3.7 years ago
GenoMax 109k

If you have not run vdb-config to set up a separate cache directory then do that first. That way you can still do cache-mgr /path_to_cache_dir -c and still keep your BAM files intact.

ADD COMMENT
0
Entering edit mode

you are a savior. Thank you so much for pointing out that I can identify a path with cache-mgr!

ADD REPLY

Login before adding your answer.

Traffic: 1507 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6