HISAT2: Question regarding providing file path to indexed genome folder
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 .
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you should use the
basenameof the index: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
Can you post the command line used to build the index?
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
There could be a problem with the index files you downloaded. Try to build your own indexes and see what happen
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.