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docker-ubuntu-snap's Issues

mmap: Cannot allocate memory

This error occurs after 4-6 hours of processing.

Environment

Snap Docker image within a Boot2Docker VM (Mac OS X).

Steps to reproduce

sirena:genomic david$ wget -O /data/projects/adamcloud/hg19/chr1.fa.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr1.fa.gz
gzip -d /data/projects/adamcloud/hg19/chr1.fa.gz

sirena:genomic david$ docker run --rm -ti -v /Users/david/data:/data gelog/snap index /data/projects/adamcloud/hg19/chr1.fa /data/projects/adamcloud/hg19/chr1.snap.idx

Output

Welcome to SNAP version 1.0beta.15.

Hash table slack 0.300000
Loading FASTA file '/data/projects/adamcloud/hg19/chr1.fa' into memory...8s
Saving genome...2s
Computing bias table.
Bias computation: 100000000 / 249251621
Bias computation: 200000000 / 249251621
Computed bias table in 3s
Allocating memory for hash tables...10s
Building hash tables.
Indexing 100000000 / 249251621
Indexing 200000000 / 249251621
mmap: Cannot allocate memory
SNAP exited with exit code 1 from line 345 of file SNAPLib/BigAlloc.cpp
sirena:genomic david$

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