HISAT2 is not working as expected

[guillepl]

Hi, I'm running this command:

  CIRIquant -t 25 \
            -v \
            -1 alignment_rrna/13_S1_unmappedreads_1.fq.gz \
            -2 alignment_rrna/13_S1_unmappedreads_2.fq.gz \
            --config ciri_quant/13_S1.yaml \
            -o ciriquant \
            -p 13_S1 \
            --circ circ_annot/13_S1_circ_known.txt \
            --tool CIRCexplorer2

With the YAML content being:

name: hg38
tools:
  bwa: "[private]/CIRIquant_env/bin/bwa"
  hisat2: "[private]/CIRIquant_env/bin/hisat2"
  stringtie: "[private]/CIRIquant_env/bin/stringtie"
  samtools: "[private]/CIRIquant_env/bin/samtools"

reference:
  fasta: hg38.fa
  gtf: hg38.ncbiRefSeq.gtf
  bwa_index: index_bwa/hg38
  hisat_index: index_hisat/hg38

And, somehow, HISAT2 BAM output is empty. The LOG file contains this error prompt:

Error: Encountered internal HISAT2 exception (#1)
Command: [private]/CIRIquant_env/bin/hisat2-align-s --wrapper basic-0 -p 25 --dta -q -x [private]/index_hisat/hg38 -t --new-summary --read-lengths 76,75,74,73,72,71,70,68,62,69,67,66,65,63,60,59,57,64,54,61,52,35,44,58,53,43,55,51,45,50,49,48,47,39,37,56,41,40,38,36,33,19 -1 /tmp/24727.inpipe1 -2 /tmp/24727.inpipe2 
(ERR): hisat2-align exited with value 1

Can someone explain where is the problem? I've tried running HISAT2 alignment myself, and it works as expected. I think the problem must be in some kind of previous step that maybe is modifying my input files. Could it be possible?