Error in running Abyss assembler for chicken genome assembly

Question

[Maliha]

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-rr.dot assembly-1.fa assembly-1.dot merged_female.fa assembly-1.fa:0: warning: file is empty make: *** [/home/mkk/.conda/envs/abyss-env/bin/abyss-pe.Makefile:583: assembly-1-rr.dot] Segmentation fault (core dumped)

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

[sainavyav22]

Hello dr. Manila, I am working on dog genome assembly using ABySS I received the error: Killed after running for 24hr it did not move any from reading the R1 in paired end sequences. Could you please share the experience of yours on this. Were you able to assemble the genome?

This is the code I used, abyss-pe name=Chester j=3 k=31 c=25 e=5 s=300 in='Chester-gDNA-paired_S12_L004_R1_001.fastq.gz Chester-gDNA-paired_S12_L004_R2_001.fastq.gz'