Hisat2 runs extremely slow

[bounlu]

Hi,

I am running the tool with the suggested commandline for the given example:

clear_quant -1 mate_1.fastq -2 mate_2.fastq -g hg38.fa -i hg38.hisat_index -j hg38.bowtie_index -G annotation.gtf -o output_dir

My code and sample:

$ clear_quant -1 205_1.fq.gz -2 205_2.fq.gz -g /library/hg19.fa -i /library/hg19.fa -j /library/hg19.fa -G /library/hg19.genes.gtf -o 205 -p 40
###Parameters:
Namespace(bowtie1='/library/hg19.fa', genome='/library/hg19.fa', gtf='/library/hg19.genes.gtf', hisat='/library/hg19.fa', m1='205_1.fq.gz', m2='205_2.fq.gz', output='205', thread='40')
###Parameters

###Start hisat2 mapping
# start to get sp sites for hisat mapping
# start to align to genome by hisat

However, it takes extremely long. The mapping step got stuck there for 3 days, still running and not sure how long it will take. Is this normal? My samples have about 100M reads on average, either RNA-Seq (ribo-) or circRNA-Seq (ribo- and RNaseR+) samples. How can I speed it up starting from the fastq files (without running CIRCexplorer2 with STAR first to get bam files)? Can you also integrate STAR aligner to the CIRCexplorer3/CLEAR?

@xingma

[bounlu]

I fixed this by changing:

-i /library/hg19.fa

to

-i /library/hg19

---

Have you tried CSI NGS Portal yet?