Question: Picard Tools runs out of space when running Poolparty pipeline
0
gravatar for Dracaena
11 months ago by
Dracaena30
Dracaena30 wrote:

Hi all,

I am using a pipeline to align and analyze NGS data called "Poolparty" ( https://github.com/StevenMicheletti/poolparty ). Overall it's a great way to do so since it delivers both VCF and sync (popoolation) files. The only problem is, that I don't have enough space in my /tmp directory and this causes issues when Picard Tools starts running. I am running linux on windows as an app (Ubuntu for windows) and the disc on which my home folder is on is tight in space. So here's my question: Is there I way to set my /tmp directory to another (external) hard drive? Or can I add an argument to the script somehow so Picard Tools knows which folder to use as TEMP folder. I know if you use Picard Tools alone you can set "TEMP_DIR path"

Many thanks

ADD COMMENTlink modified 11 months ago • written 11 months ago by Dracaena30

I know if you use Picard Tools alone you can set "TEMP_DIR path"

so, why don't you use this parameter ?

ADD REPLYlink written 11 months ago by Pierre Lindenbaum123k

One can set a temporary folder for Picard (see Out Of Disk Space With Picard Tools ? and picard-tools MarkDuplicates - spilling to disk). You may have to hack PoolParty, but it should be pretty easy to add a command-line option to it.

You can also try the suggestion from How to change default /tmp to /home/user/tmp.

ADD REPLYlink written 11 months ago by h.mon27k
0
gravatar for Dracaena
11 months ago by
Dracaena30
Dracaena30 wrote:

Ok guys, I just tried adding the TMP_DIR in the config file and it worked. Picard Tools used that DIR as temp. Poolparty does not mention that this is possible, but apparantly it is. Nice!

ADD COMMENTlink written 11 months ago by Dracaena30
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