Question

Running Hisat2 but it seems not working at all

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2.5 years ago

chansik ▴ 10

I'm running Hisat2 with the code below:

hisat2 -p 9 -f ../0.Reference/CHO-PICRH -1 ../2.Trimmomatic/ERR2593198_1_trimmed.fastq.gz -2 ../2.Trimmomatic/ERR2593198_2_trimmed.fastq.gz 2> ../3.HISAT/ERR25593198.log| samtools view -Sbo ../3.HISAT/ERR2593198.bam

It's been running over 24 hours but it doesn't seem work well.

Can you please check the code above and help me solve the problem? (I also attached a screen capture)

Thanks,

enter image description here

HISAT2 Mapping RNA-seq • 1.3k views

ADD COMMENT • link updated 2.5 years ago by Istvan Albert 100k • written 2.5 years ago by chansik ▴ 10

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Have you opened another terminal to 1) check that log file you are creating for errors or progress messages and 2) use top or htop to take a look at running processes?

ADD REPLY • link 2.5 years ago by WouterDeCoster 47k

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yes, hisat2+ is keep running for several hours on 'top' but as shown in the screen capture, the .log is empty

ADD REPLY • link 2.5 years ago by chansik ▴ 10

score 0 · Answer 1 · 2021-10-30

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2.5 years ago

Istvan Albert 100k

as far as I know hisat2 takes the index via the -x flag

how come your command line does not list that flag

then you are passing the -f flag (FASTA query) but your input is in (FASTQ)

ADD COMMENT • link 2.5 years ago by Istvan Albert 100k

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Thanks for your comment Istvan.

I didn't realize the typo. it should be -x, not -f.

thanks again!

ADD REPLY • link 2.5 years ago by chansik ▴ 10