Pipeline fails using test data

[kirstyjamieson]

Hi Jin,
The atac-seq pipeline fails at BackgroundConfigAsyncJobExecutionActor. I'm also getting a warning that "Localization via hard link has failed". Attached is my script and the output. I'm using coda version 4.5.11 and the .json file you provide.

Thanks,
Kirsty

run.sh.txt
run.sh.o489151.txt

[leepc12]

Did you follow the instruction (step 3 and 4) on https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/tutorial_sge.md? Pipeline failed to find genome database for a test sample.
Also reduce -Xmx16384M to 1GB or 2GB. It's too big.

[kirstyjamieson]

Yes, I had downloaded the genome database and test sample data. I checked the directories and discovered missing files and folders after the run failed. Somehow running the pipeline caused this. I downloaded everything again and reran and it worked. Not sure if this is a problem on my cluster or a bug with the pipeline. I'll let you know if it happens again.

[leepc12]

@kirstyjamieson: I see. BTW you can simply ignore the warning Localization via hard link has failed. If that fails then it automatically switches to soft link or physical copy.

[kirstyjamieson]

Thanks, good to know!