alignment with HISAT2

Question

[blooming.daisy333]

i am using following command to align the reads in hisat2: for my project

[memona@farooq hisat2-2.1.0]$ ./hisat2 –p 64 --max-intronlen 10000 –x /data/memona/hisat2-2.1.0/hisat_index -1 /data/memona/SRR959590_A_1P.fq -2 /data/memona/SRR959590_A_2P.fq –S /data/memona/hisatresult/hisat_align.sam

and getting this error.:

Warning: Output file '64' was specified without -S.  This will not work in future HISAT 2 versions.  Please use -S instead.
Extra parameter(s) specified: "–x", "/data/memona/hisat2-2.1.0/hisat_index", "–S", "/data/memona/hisatresult/hisat_align.sam"
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)
Command: /data/memona/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 --max-intronlen 10000 -1 /data/memona/SRR959590_A_1P.fq -2 /data/memona/SRR959590_A_2P.fq –p 64 –x /data/memona/hisat2-2.1.0/hisat_index –S /data/memona/hisatresult/hisat_align.sam
(ERR): hisat2-align exited with value 1

-p 64 is not a file but number of threads im using. further i want all the output files in hisatresult directory as is spesified in command line.. kindly help me to resolve the issue.

Answer 1

[Devon Ryan]

The - in -p is an em-dash, not a hyphen, in your command. I imagine you copied and pasted from Word or something like that that "autocorrected" it for you. Just type the command manually and that should resolve the error.

[blooming.daisy333]

thank you so much Devon. you ve correctly pointed out the mistake. it worked