Entering edit mode
6.2 years ago
Mbillah
▴
140
abyss is still running more than 24 hours, but not produce any output. My command is :
abyss-pe name=goat k=52 np=8 j=8 in='/data/masum/bowtie2/b143_1.fq /data/masum/bowtie2/b143_2.fq'
Number of paired read : 140958110
How much time is needed ? Will the output file come at a time after finishing the process? How can I understand that the process is running properly though I saw that on the top in abyss by 8 process.
TIA
You are missing the final
'in your command. I know you probably just copied it wrong over to here, but just want to point that out in case you missed it. I would give it some more time to run, it is a pretty big task. It could be writing tmp files somewhere, or just has everything loaded to memory. Just some ideas -- I'm no expert.Thank you for your reply
What's the estimated genome size of your organism? And how many reads do you have?
Number of reads: 140 M. Estimated genome size: 2.9 G