Abyss run time

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5.5 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

assembly abyss • 1.6k views

ADD COMMENT • link 5.5 years ago by Mbillah ▴ 140

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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.

ADD REPLY • link 5.5 years ago by goodez ▴ 640

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Thank you for your reply

ADD REPLY • link 5.5 years ago by Mbillah ▴ 140

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What's the estimated genome size of your organism? And how many reads do you have?