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Abyss taking a Long time to run

I am trying to do genome assembly of a chicken using Abyss with the following command-

abyss-pe k=64 np=8 j=8 name=assembly_female in='s1.fastq s2.fastq'

However, even after three hours, the process is still stuck in the same place like this-

/home/mkkk/.conda/envs/abyss-env/bin/mpirun -np 8 ABYSS-P -k64 -q3    --coverage-hist=coverage.hist -s assembly_female-bubbles.fa  -o assembly_female-1.fa s1.fastq s2.fastq 
ABySS 2.3.5
ABYSS-P -k64 -q3 --coverage-hist=coverage.hist -s assembly_female-bubbles.fa -o assembly_female-1.fa s1.fastq s2.fastq
Running on 8 processors
0: Running on host cs1
1: Running on host cs1
2: Running on host cs1
3: Running on host cs1
4: Running on host cs1
5: Running on host cs1
6: Running on host cs1
7: Running on host cs1
0: Reading `s1.fastq'...
1: Reading `s2.fastq'...

What should I change?

abyss assembly genome fastq
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written by Maliha • Maliha

Depending on the size of your input data assembly jobs can take hour(s) (even days). As long as long you have no other error/have enough hardware resources available waiting patiently is going to be the best option.

• 0 views • link
written by GenoMax GenoMax

The size of my input data is 48.02 GB. Is it going to take one day or several days?

• 0 views • link
written by Maliha • Maliha

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