Question: Could not locate a HISAT2 index to basename
1
gravatar for oolongoni
2.4 years ago by
oolongoni10
United States
oolongoni10 wrote:

First time trying out HISAT2 and I'm having a problem here, even with the pre-made indices for GRCH38.

$ hisat2 -x /share/projects/RNASeq/data/reference/GRCh38/grch38_tran -1 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R1_001.fastq.gz -2 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R2_001.fastq.gz -S tmp.sam

Error follows

Could not locate a HISAT2 index corresponding to basename "/share/projects/RNASeq/data/reference/GRCh38/grch38_tran"
Error: Encountered internal HISAT2 exception (#1)
Command: /home/echang/software/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 -S tmp.sam -1 /tmp/31969.inpipe1 -2 /tmp/31969.inpipe2 /share/projects/RNASeq/data/reference/GRCh38/grch38_tran
(ERR): hisat2-align exited with value 1

The contents of the grch38_tran

$ ls /share/projects/RNASeq/data/reference/GRCh38/grch38_tran
genome_tran.1.ht2  genome_tran.3.ht2  genome_tran.5.ht2  genome_tran.7.ht2  make_grch38_tran.sh
genome_tran.2.ht2  genome_tran.4.ht2  genome_tran.6.ht2  genome_tran.8.ht2

I thought perhaps the genome_tran.*.ht2 needed to change to grch38_tran.*.ht2, but it still does not work after renaming. I've since untarred the original file again without change. Was there a step I missed? Where can I find HISTAT2_INDEXES?

-x <hisat2-idx>
The basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final .1.ht2 / etc. hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2_INDEXES environment variable.
hisat2 rna-seq • 4.4k views
ADD COMMENTlink modified 6 months ago by zhiminfdu0 • written 2.4 years ago by oolongoni10

"/share/projects/RNASeq/data/reference/GRCh38/grch38_tran " maybe has some problem. you could try to change the path into "~/share/projects/RNASeq/data/reference/GRCh38/grch38_tran". Totally, you should know its correct directory.

ADD REPLYlink written 6 months ago by zhiminfdu0

That's not the same. ~ is shorthand for your home directory, while /share is likely to exist on the root. Note that this question also already has an answer.

ADD REPLYlink written 6 months ago by WouterDeCoster42k
1
gravatar for EagleEye
2.4 years ago by
EagleEye6.5k
Sweden
EagleEye6.5k wrote:

Your genome index path in hisat2 should be,

-x /share/projects/RNASeq/data/reference/GRCh38/grch38_tran/genome_tran
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by EagleEye6.5k

Thank you sir! I guess it makes sense now. I wonder why renaming the *ht2 index files did not work.

ADD REPLYlink written 2.4 years ago by oolongoni10
0
gravatar for lakhujanivijay
2.4 years ago by
lakhujanivijay4.6k
India
lakhujanivijay4.6k wrote:

Instead of renaming the index files, could you try changing the index prefix itself in the -x option like shown below?

$ hisat2 -x /share/projects/RNASeq/data/reference/GRCh38/genome_tran -1 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R1_001.fastq.gz -2 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R2_001.fastq.gz -S tmp.sam

Give a try and let us know the outcome.

ADD COMMENTlink written 2.4 years ago by lakhujanivijay4.6k

Thanks for your input! I can try changing the index directory name from /share/projects/RNASeq/data/reference/GRCh38/grch38_tran/ to /share/projects/RNASeq/data/reference/GRCh38/genome_tran after the job is finished running.

ADD REPLYlink written 2.4 years ago by oolongoni10

I have the same problem but adding the file prefix to the path is not solving it :/ . I still have the same problem, do you know why could it be? Here I leave you my code (RNA-seq mapping, single end mode, Mac OS X El Capitan, HiSat2): hisat2 -f --no-softclip -x /Users/dpz/Documents/Ref/hisat2index/hisat2indexhg38 -U path/to/data/reads.fastq.gz -S output.sam

ADD REPLYlink modified 19 months ago • written 19 months ago by msimmer92210
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