How can i solve hisat2 error?

Question

[Chan]

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?

[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

[finswimmer]

Hello Chan,

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

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

Thank you!

Answer 1

[finswimmer]

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