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

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

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written 5.8 years ago by mailard •

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

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written 5.8 years ago by ATpoint

I cant say but its WGS of hepG2

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written 5.8 years ago by mailard •

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)

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written 5.8 years ago by lieven.sterck

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

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written 5.8 years ago by mailard •

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.

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written 5.8 years ago by ATpoint

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

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written 5.8 years ago by mailard •

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

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written 5.8 years ago by lieven.sterck

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

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written 5.8 years ago by ATpoint

Its just sleeeping, not running. I dont know( Its 59gb

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written 5.8 years ago by mailard •

Its just sleeping, not running. I dont know( Its 59gb and yup, any error

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written 5.8 years ago by mailard •

0 answers

No answers yet.

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