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5.1 years ago
673219368
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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
Do you actually run
/home/xxx/tools/Hisat2/hisat2-2.1.0/hisat2-align-s
or do you just usehisat2
as executable? Does your output directory exist, and do you have write permission?I finally solved the problem. Just output the file to the root directory. It may be a bug.