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HISAT2 - "Encountered internal HISAT2 exception (#1)"

Hello everyone!

I am a noob in bioinformatics. Now I am trying to run "new Tuxedo" protocol using HISAT. But I have the following problem:

Error: Encountered internal HISAT2 exception (#1) Command: /opt/cesga/hisat2/2.0.5/gcc/5.3.0/bin/hisat2-align-s --wrapper basic-0
-p 8 --dat -x GRCh38/grch38/genome -S Hsa002F_L.sam -U samples/original/females/lti/Hsa002F_L.fastq  (ERR): hisat2-align exited with value 1

We have several transcriptomes sequenced using IonTorrent (single-end) from different biological conditions. I have tried to run HISAT with the following command:

hisat2 -p 8 --dat -x grch38/genome -U $SAMPLES/Hsa002F_L.fastq -S Hsa002F_L.sam

I have downloaded the index from HISAT webpage.

Thanks in advance.

rna-seq alignment software error genome
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written by manuelmendoza • manuelmendoza

Hello manuelmendoza!

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written by manuelmendoza • manuelmendoza

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