Question: Question: Error: Could not open alignment output; Encountered internal HISAT2 exception (#1)
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gravatar for 673219368
19 months ago by
6732193680
6732193680 wrote:

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

rna-seq hisat • 1.3k views
ADD COMMENTlink modified 19 months ago by lakhujanivijay5.2k • written 19 months ago by 6732193680

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?

ADD REPLYlink written 19 months ago by WouterDeCoster44k

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

ADD REPLYlink written 18 months ago by 6732193680
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