Error in running Abyss assembler for chicken genome assembly
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4 months ago
Maliha ▴ 20

I have a Fasta file of the chicken genome sequence which size is 54 GB. I am trying to do the assembly of this chicken genome using Abyss using the following code-

abyss-pe k=32 B=25G name=assembly in='merged_female.fa'

I gave B=25G as the chicken genome has around 1.2 × 10^9 base pairs and k=32 to reduce memory usage. I have 122Gi memory available in the system. I got this error-

abyss-rresolver-short -b25G -f0.8 -j2 -k32 \ -h assembly-1-rr --dot -c assembly-1-rr.fa \ -g assembly-1.fa merged_female.fa assembly-1.fa:0: warning: file is empty make: *** [/home/mkk/.conda/envs/abyss-env/bin/abyss-pe.Makefile:583:] Segmentation fault (core dumped)

I'd be thankful if someone can give me a solution for this problem.

abyss assembly genome fasta • 266 views

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