Hisat2 error: --read-lengths arg must be at least 20

Question

[aindap]

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.

[ATpoint]

I cannot reproduce this. Is this the exact command line or are you running from within a script or workflow? The option -hisat2.sam that the wrapper reports is suspicious and I think should not be there, therefore the question if your command is 100% what you used. I could not find -hisat2.sam anywhere in the source code. Please also share a head of your fastq files.

[sifanye1997]

can you tell me how do you solve your problems？i met the same situation. you said your fastq were not minimum length,so you change your fastq(s) or change the parameter of the hisat2?

[ATpoint]

I will have to filter for length before running. Problem solved.

What is unclear from this answer? OP removed reads with low read length.

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Answer 1

[aindap]

Oooof - this is what happens when you try and do work late at night and exhausted. Yes, I does seem some sequences in my fastq(s) were not minimum length. I will have to filter for length before running. Problem solved. Thanks for your reply.

[dariober]

I also got this error with hisat2 v2.2.0 but v2.1.0 works fine. Must be a recent change...?