Running Hisat2 but it seems not working at all

Question

[chansik]

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,

[WouterDeCoster]

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?

[chansik]

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

Answer 1

[Istvan Albert]

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)

[chansik]

Thanks for your comment Istvan.

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

thanks again!