Entering edit mode
8 days ago
Maliha
▴
20
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?
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.
The size of my input data is 48.02 GB. Is it going to take one day or several days?