Could not locate a HISAT2 index to basename
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4.3 years ago
oolongoni ▴ 10

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.

RNA-Seq Hisat2 • 8.0k views
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"/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.

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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.

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4.3 years ago
EagleEye 7.1k

Your genome index path in hisat2 should be,

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

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

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4.3 years ago

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.

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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.

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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