HISAT2: Question regarding providing file path to indexed genome folder

Question

[m90]

hisat2 -p 1 -x hisatIndex/genome.fa --dta --rna-strandness RF -1 $R1 -2 $R2 -S genome.sam(ERR): "hisatIndex/genome.fa" does not exist Exiting now ... this error showing up every time i run the code and I dont know what is the problem ? note : that genome.fa is actually in histIndex folder .

[andres.firrincieli]

you should use the basename of the index:

hisat2 -p 1 -x hisatIndex/genome --dta --rna-strandness RF -1 $R1 -2 $R2 -S genome.sam

[m90]

i edit it and this what i got Error: Encountered exception: 'std::bad_alloc' Command: /home/mariam/miniconda3/envs/ngs1/bin/hisat2-align-s --wrapper basic-0 -p 1 -x hg19/genome --dta --rna-strandness RF -S genome.sam --read-lengths 101 -1 /tmp/14187.inpipe1 -2 /tmp/14187.inpipe2 (ERR): hisat2-align exited with value 1

[andres.firrincieli]

Can you post the command line used to build the index?

[m90]

hisat2 -p 1 -x hg19/genome --dta --rna-strandness RF -1 $R1 -2 $R2 -S genome.sam

i just want to explain something that I downloaded indexed hg19 by hisat2 so, start alignment directly

[andres.firrincieli]

There could be a problem with the index files you downloaded. Try to build your own indexes and see what happen

[ATpoint]

-1 /tmp/14187.inpipe1 -2 /tmp/14187.inpipe2

This looks unusual, how do you provide the files to the command, so what are these R1/R2 variables? In general when you have odd errors try to first run the command manually on a small subset of reads to sort out software/index problems and then take care of a potentially flawed script.