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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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Java memory issue #124

Open ahorn720 opened 6 years ago

ahorn720 commented 6 years ago

I think that my directory should have enough memory, im not getting a quota error like previously. Because i thought it was a java memory issue, i even added export _JAVA_OPTIONS="-Xms256M -Xmx728M -XX:ParallelGCThreads=1" to my ~/.bashrc too. But im still getting this error. Previously it would stop at bowtie but now its stopping at the adapter cutting.

Any suggestions?

Thank you! NBM_15-4stderror.txt NBM_15-4stdout.txt

leepc12 commented 6 years ago

This is a disk space problem. Please check disk space on

1) your working directory where you ran the pipeline command line. 2) your pipeline git directory (/home/$USER usually have small space). 3) temporary directories ($TMP and $TMPDIR).