Question: Error: Could not open alignment output; Encountered internal HISAT2 exception (#1)

Question

[673219368]

Hello, I am using HISAT2 for aligning transcripts to the reference genome. I run the following commands and then get errors:
Error: Could not open alignment output file Error: Encountered internal HISAT2 exception (#1)

$ /home/xxx/tools/Hisat2/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 -p8 -x Hisat2index -S /home/xxx/liquorice/Hisat2Result/CT18TN1.sam -1 /home/xxx/liquorice/liquoriceTrimResult/CT18TN1/R1.clean.fastq -2 /home/xxx/liquorice/liquoriceTrimResult/CT18TN1/R2.clean.fastq

Kindly help

[WouterDeCoster]

Do you actually run /home/xxx/tools/Hisat2/hisat2-2.1.0/hisat2-align-s or do you just use hisat2 as executable? Does your output directory exist, and do you have write permission?

[673219368]

I finally solved the problem. Just output the file to the root directory. It may be a bug.