HISAT2: Question regarding providing file path to indexed genome folder
0
0
Entering edit mode
5 months ago
m90 ▴ 30

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 .

hisat2 alignment indexed • 546 views
ADD COMMENT
0
Entering edit mode

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
ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

-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.

ADD REPLY

Login before adding your answer.

Traffic: 1264 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6