I'm struggling with this issue:


    ./hisat2 -x ../../data/index/hisat_2/iwgsc -U ../../data/mrcv/genes/21dpi_C_R1.fq.gz,../../data/mrcv/genes/21dpi_C_R2.fq.gz,../../data/mrcv/genes/21dpi_C_R3.fq.gz,../../data/mrcv/genes/21dpi_C_R4.fq.gz,../../data/mrcv/genes/21dpi_T_R1.fq.gz,../../data/mrcv/genes/21dpi_T_R2.fq.gz,../../data/mrcv/genes/21dpi_T_R3.fq.gz,../../data/mrcv/genes/21dpi_T_R4.fq.gz -S ../../data/mrcv/genes/alignment/21.sam --un ../../data/mrcv/genes/alignment/21UN.sam -p 6 
    
    Error: Read J00113:78:H3JKNBBXX:3:2209:5670:2281 1:N:0:CGATGT has more quality values than read characters.
    terminate called after throwing an instance of 'int'
    Aborted (core dumped)
    (ERR): hisat2-align exited with value 134

Scythe was used to remove adapter contamination and Sickle to remove low-quality reads. 

I'm using HISAT2 version 2.1.0 on Ubuntu 18.04. Any ideas what could be wrong?
I could verify with 

    gzip -t R2.fq.gz && echo ok || echo bad 

that the file was corrupted. For some reason the reads were not in the correct line. Re-downloading the file solved the issue. 
