OutOfMemoryError

[flangelier]

Error:

2015-03-22 17:29:25 ERROR Executor:96 - Exception in task 0.0 in stage 1.0 (TID 16)
java.lang.OutOfMemoryError: GC overhead limit exceeded

Step to reproduce:

docker run -ti --rm --name client-genomics -v /data:/data gelog/avocado /bin/bash avocado-submit /data/SRR062634.adam /data/chr1.fa /data/SRR062634.avr /usr/local/avocado/avocado-sample-configs/basic.properties

You can get the files by following the step from :

• snap
• adam

[sebastienbonami]

Have you try reducing the executor and driver memory in Spark? See: GELOG/adamcloud#11 (comment)

[davidonlaptop]

How did you generate SRR062634.adam?

• Please describe the ADAM commands as well (URL of original data, command used to run ADAM).

[flangelier]

If order, you have to :

Getting the index

mkdir -p /data/
wget -O /data/chr1.fa.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr1.fa.gz
gzip -d /data/chr1.fa.gz

Indexing with snap

docker run --rm=true -ti -v /data:/data gelog/snap index /data/chr1.fa /data/snap-index.chr1

Getting the chromosome

wget -O /data/SRR062634.filt.fastq.gz ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00096/sequence_read/SRR062634.filt.fastq.gz
gzip -d /data/SRR062634.filt.fastq.gz

Aligning the chromosome

docker run --rm=true -ti -v /data:/data gelog/snap single /data/snap-index.chr1/ /data/SRR062634.filt.fastq -o /data/SRR062634.sam

Running adam

docker run --rm=true -ti -v /data/:/data gelog/adam adam-submit transform /data/SRR062634.sam /data/SRR062634.adam

You should now have all the needed files

[davidonlaptop]

The file SRR062634.filt.fastq.gz file contains the bogus reads that have been filtered out after quality control.

Try to feed this file to ADAM:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00096/alignment/HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20120522.bam