Help with ABySS use
Hi, I used the following command to perform denovo genome assembly of my paired-end reads.
abyss-pe name=Chester j=3 k=31 e=5 c=30 s=300 in='Chester-gDNA-paired_S12_L004_R1_001.fastq.gz Chester-gDNA-paired_S12_L004_R2_001.fastq.gz'
I ran the abyss for 24hr, but I only got unting and conting files (Chester-unitigs.fa Chester-contigs.fa). The scaffold file was not generated. Is there anything I need to change in my coammand? Can someone please assist me with this?
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sainavyav22 •
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Did the job complete?
No, it did not. Do I need to extend the time.
Are you required to set a specific time on your jobs? If the program did not finish then you will have to restart/re-run with an extended time. Assemblers can take a while to run with large genomes like human.
Yes! I am using the slurm resources so I have to set the time. I will re-run with an extended time and let you know the results. Thank you very much!