Is it normal that Trimmomatic is trimming DNA seq 2 days?

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4.1 years ago

mailard ▴ 30

Hi! I run trimmomatic

java -jar /home/user/program/Trimmomatic-0.39/trimmomatic-0.39.jar SE -phred33 h_2.fastq.gz output2.fastq.gz HEADCROP:11 CROP:149

And this code is working 2 days. Is it normal?

dna trimmomatic • 1.3k views

ADD COMMENT • link 4.1 years ago by mailard ▴ 30

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Intuituvely I'd say no. How many reads in the file?

ADD REPLY • link 4.1 years ago by ATpoint 85k

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I cant say but its WGS of hepG2

ADD REPLY • link 4.1 years ago by mailard ▴ 30

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I'm with ATpoint on this, unless you're running this on your smartphone or such, then it could be (but still not very likely)

ADD REPLY • link 4.1 years ago by lieven.sterck 15k

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No, i run on my computer :) Maybe i have a mistake in my code?

ADD REPLY • link 4.1 years ago by mailard ▴ 30

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Is it even running? Check with top, maybe it hang up and failed to exit properly. What is the size of the trimmed file currently, is it growing, ise ls -l to check.

ADD REPLY • link 4.1 years ago by ATpoint 85k

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No, its not running! Do i need restart the command?

ADD REPLY • link 4.1 years ago by mailard ▴ 30

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I would say yes, but it is also important to figure out why it stop (/is no longer) running .

ADD REPLY • link 4.1 years ago by lieven.sterck 15k

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Come on, give some details. Did it even start, is there an output file, how big is it, any errors in the log?