Could not locate a HISAT2 index to basename

Question

[oolongoni]

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.

[zhiminfdu]

"/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.

[WouterDeCoster]

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.

[יובל]

Hi i have the same problem i tried the path from here it dose not work for me. would like your kindly help pleas :)

pwd@DESKTOP-HDAGSMU:/mnt/c/Users/User/Desktop/genomics_and_bioinformatics/project$ hisat2-align-s -x /grch38_tran/genome_tran -U DE1a_subsample_trimmed.fastq.gz -S DE1a_subsample_mapped.sam

Could not locate a HISAT2 index corresponding to basename "/grch38_tran/genome_tran" Error: Encountered internal HISAT2 exception (#1) Command: hisat2-align-s -x /grch38_tran/genome_tran -U DE1a_subsample_trimmed.fastq.gz -S DE1a_subsample_mapped.sam

[GenoMax]

What does ls -lh /grch38_tran/genome_tran* show?

[יובל]

it is actually just grch38_tran

ls -lh /grch38_tran shows "No such file or directory".

but it is decently in there!

[יובל]

Hi and thanks, I tried using the whole phtw and it worked, this error is gone but the code still doesn't work now I just have one more error

I would appreciate further help please

The command now is

hisat2-align-s -x /mnt/c/Users/User/Desktop/genomics_and_bioinformatics/projectgrcm38_tran -U DE1a_subsample_trimmed.fastq.gz -S DE1a_subsample_mapped.sam

and i gate back

Error: Encountered internal HISAT2 exception (#1)

[GenoMax]

Did you make projectgrcm38_tran index yourself?

Run HISAT2 directly like so

hisat2 -x /mnt/c/Users/User/Desktop/genomics_and_bioinformatics/projectgrcm38_tran -1 DE1a_subsample_trimmed.fastq.gz -S DE1a_subsample_mapped.sam

You need to use -1 if you have a single data file. -U option is where you have multiple filenames listed in another file.

[יובל]

actually I already tried it without the U: hisat2-align-s -x grcm38_tran/genome_tran -1 DE1a_subsample_trimmed.fastq -S DE1a_subsample_mapped.sam and I think it worked (I got some kind of sam file, that's called DE1a_subsample_mapped.sam) but I'm not sure that there really was a proper mapping.

In this way as you mentioned: hisat2-align-s -x grcm38_tran/genome_tran -1 DE1a_subsample_trimmed.fastq -S DE1a_subsample_mapped.sam

Returns it: Error: 1 mate files/sequences were specified with -1, but 0 mate files/sequences were specified with -2. The same number of mate files/ sequences must be specified with -1 and -2. Error: Encountered internal HISAT2 exception (#1) Command: hisat2-align-s -x grcm38_tran/genome_tran -1 DE1a_subsample_trimmed.fastq -S DE1a_subsample_mapped.sam

Answer 1

[EagleEye]

Your genome index path in hisat2 should be,

-x /share/projects/RNASeq/data/reference/GRCh38/grch38_tran/genome_tran

[oolongoni]

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

Answer 2

[lakhujanivijay]

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.

[oolongoni]

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.

[msimmer92]

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