I am new to Hisat2 and I am trying to align paired-end rnaseq fastq files with hisat2 v 2.2.0. I downloaded the hg38 transcriptome index from the software homepage. My command is:
hisat2 -x genome_tran -p 8 -1 1.fastq.gz -2 2.fastq.gz | samtools view -bS - > hisat2.bam
I get the following error message. I checked to see if my fastq files were corrupted, but they seem fine. I'm pretty perplexed as to what is going on because my command line seems to follow the manual. Can you please help me out?
--read-lengths arg must be at least 20 <followed by hisat2 options> Error: Encountered internal HISAT2 exception (#1) Error: Encountered internal HISAT2 exception (#1) Command: hisat2-align-s --wrapper basic-0 -p 8 -x genome_tran -hisat2.sam --read-lengths 76,75,74,73,72,71,70,69,67,61,65,68,66,62,58,53,48,64,63,59,57,56,54,60,55,50,45,27,21,14 -1 /tmp/33180.inpipe1 -2 /tmp/33180.inpipe2 (ERR): hisat2-align exited with value 1
I'm not sure what is going on and if anyone can help point me in the right direction that would be great.