Entering edit mode
11.3 years ago
DG
7.3k
Does anyone have experience running the ddRAD pipeline of Peterson et al? I'm running on a MiSeq run of data and the amount of disk space it seems to require is huge. I modified one of the files so that it deletes BLAT files, which helps, but the intermediate *.label files, which will be required for the MCL step, are also approaching a few hundred MB to close to a GB each per query (I have the sequences split in to 4000 query files).
I could try reducing the number of individuals from the samples, which may be my only option.
Hi,Dan. Maybe you can run it with --cleanup method!
I did, the problem is that the the files in question are necessary at the next step, after which cleanup would be invoked. I also had to go in and manually set a flag to not keep the Blat files in the code. It is a boolean option hardcoded as TRUE with checks in the code for what to do if it is false, but the flag can;t be set by an external option.