sparsehash FATAL ERROR: failed to allocate 19 groups

[mictadlo]

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,

Michal

[jwcodee]

Can you tell me the ram capacity of your machine?

[mictadlo]

480 GB

[jwcodee]

There can be two reasons for your error. One is if you are using a 32bit executable. You can try this command file -Lwhich ABYSS`` and report the output. The other being your machine does not have enough memory. You run the bloom filter mode to alleviate the memory issue. You can look at this section for a simple example https://github.com/bcgsc/abyss#assembling-using-a-bloom-filter-de-bruijn-graph.

[mictadlo]

Thank you, the memory was an issue.