sparsehash FATAL ERROR: failed to allocate 19 groups

Question

[Ric]

HI

Please report

$ abyss-pe version
abyss-pe (ABySS) 2.2.4
$ lsb_release -d
Description:    Ubuntu 18.04.1 LTS

Assembly error

complete abyss-pe command line

export TMPDIR=/mnt/volume1/abyss-96-fastp/tmp
mkdir $TMPDIR

abyss-pe k=96 name=16c-96 lib='pea peb pec ped' pea='../L001_R1.fastp.fastq ../L001_R2.fastq' peb='../L002_R1.fastq ../L002_R2.fastq'  pec='../L003_R1.fastq ../L003_R2.fastq' ped='../L004_R1.fastq ../L004_R2.fastq' j=62

output of abyss-pe

ABYSS -k96 -q3    --coverage-hist=coverage.hist -s 16c-96-bubbles.fa  -o 16c-96-1.fa ../16c/L001_R1.fastq ../16c/L001_R2.fastq ../16c/L002_R1.fastq ../16c/L002_R2.fastq ../16c/L003_R1.fastq ../16c/L003_R2.fastq ../16c/L004_R1.fastq ../16c/L004_R2.fastq
ABySS 2.2.4
ABYSS -k96 -q3 --coverage-hist=coverage.hist -s 16c-96-bubbles.fa -o 16c-96-1.fa ../16c/L001_R1.fastq ../16c/L001_R2.fastq ../16c/L002_R1.fastq ../16c/L002_R2.fastq ../16c/L003_R1.fastq ../16c/L003_R2.fastq ../16c/L004_R1.fastq ../16c/L004_R2.fastq
Reading `../16c/L001_R1.fastq'...
`../16c/L001_R1.fastq': discarded 276594 reads shorter than 96 bases
`../16c/L001_R1.fastq': discarded 8983 reads containing non-ACGT characters
Reading `../16c/L001_R2.fastq'...
`../16c/L001_R2.fastq': discarded 341212 reads shorter than 96 bases
`../16c/L001_R2.fastq': discarded 25613 reads containing non-ACGT characters
Reading `../16c/L002_R1.fastq'...
`../16c/L002_R1.fastq': discarded 273164 reads shorter than 96 bases
`../16c/L002_R1.fastq': discarded 10904 reads containing non-ACGT characters
Reading `../16c/L002_R2.fastq'...
`../16c/L002_R2.fastq': discarded 348890 reads shorter than 96 bases
`../16c/L002_R2.fastq': discarded 27100 reads containing non-ACGT characters
Reading `../16c/L003_R1.fastq'...
sparsehash FATAL ERROR: failed to allocate 19 groups
make: *** [/home/ubuntu/miniconda3/envs/abyss/bin/abyss-pe.Makefile:554: 16c-96-1.fa] Error 1

What did I miss?

Thank you in advance,

[colindaven]

Don't know, but maybe monitor RAM up to where it crashes. Try a simple tool like gotop or just use htop manually.

Answer 1

[john]

Answered in https://github.com/bcgsc/abyss/issues/317