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.
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written
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blooming.daisy333 •
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.
thank you so much Devon. you ve correctly pointed out the mistake. it worked
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