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How can i solve hisat2 error?

hello, im going to use hisat2 instead of tophat2.

but, i cant solve "

(ERR): hisat2-align exited with value 1 and 

Error: Encountered internal HISAT2 exception (#1)

/home/gdl/RNAseqA_2/BIN/hisat2-2.1.0/hisat --tmo -p 14 --summary-file -rg-id name /home/gdl/RNAseqA_2/BIN//hg19/genome --known-splicesite-infile /home/gdl/RNAseqA_2/BIN/hg19/Annotation.txt -1 /home/gdl/RNAseqA_2/Ground/1_Control_1_val_1.fq,gz -2 /home/gdl/RNAseqA_2/BIN/Ground/1_Control_2_val_2.fq.gz   -S Control_1 | samtools view -bS -> Control_1.hisat.bam

what is the problem?

rna-seq
• 4,228 views • link
updated by finswimmer finswimmer • written by Chan • Chan 
Extra parameter(s) specified: "Control_1"
Note that if <mates> files are specified using -1/-2, a <singles> file cannot
also be specified.  Please run bowtie separately for mates and singles.
Error: Encountered internal HISAT2 exception (#1)


(ERR): hisat2-align exited with value 1
• 1 views • link
updated by finswimmer finswimmer • written by Chan • Chan

Hello Chan,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

If you had additional informations please edit your original post or add this informations as a comment.

Thank you!

• 1 views • link
written by finswimmer finswimmer

1 answer

Hello Chan,

your parameters are not set correctly. Type hisat2 --help and have a look at them.

  • --summary-file expect a file name where to write the summary
  • -rg-id name must be --rg-id name
  • the reference genome must be introduced by -x
  • there is a typo in the filename /home/gdl/RNAseqA_2/Ground/1_Control_1_val_1.fq,gz. It must be fq.gz
  • As you pipe to samtools, don't use -S Control_1 as this writes to a file and not to stdout

fin swimmer

• 1 views • link
written by finswimmer finswimmer

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