Hisat2 error: unrecognized argument --sra-acc

Question

[farberch]

Hello,

I'm running hisat2 (version 2.0.1-beta) on a mac (OS X Yosemite, 10.10.5). It is working well on SRA data that I've downloaded and converted to fastqs. I would like to download data directly from SRA using the --sra-acc option. Here is what I'm running: time hisat2 -x /Volumes/LaCie/hg38.ref/INDEX --sra-acc SRR3192527 -S /Volumes/LaCie/bams/SRR3192527.sam. However, when I try I get the following error: hisat2-align-s: unrecognized option `--sra-acc'. I've installed the ncbi-ngs-toolkit. Any idea what might be going wrong?

Thanks!

[GenoMax]

It appears that the error is coming from HISAT2. Are you using the latest version (what does hisat2 --version show)? I am not sure if the --sra-acc option was added in later versions of HISAT2.

[farberch]

I'm going to update...

[farberch]

Turns out it works with 2.0.1 or higher...I had 2.0.1-beta...installed 2.0.4 and it works! Thanks!

Answer 1

[WouterDeCoster]

You followed those instructions when installing?

For the support of SRA data access in HISAT2, please download and install the NCBI-NGS toolkit. When running make, specify additional variables as follow. make USE_SRA=1 NCBI_NGS_DIR=/path/to/NCBI-NGS-directory NCBI_VDB_DIR=/path/to/NCBI-NGS-directory, where NCBI_NGS_DIR and NCBI_VDB_DIR will be used in Makefile for -I and -L compilation options. For example, $(NCBI_NGS_DIR)/include and $(NCBI_NGS_DIR)/lib64 will be used.

[GenoMax]

Let's give @farberch the benefit of doubt. OP did say I've installed the ncbi-ngs-toolkit.

[WouterDeCoster]

I actually referred to the make instructions, but apparently changing that didn't make a difference either. Whatever, solved now.

Answer 2

[farberch]

I went back and reinstalled the ncbi-ngs-toolkit specifying the additional variables and it still didn't work....

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts. SUBMIT ANSWERS should only be used for new answers to original question.