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gear-genomics / dicey

In-silico PCR, primer design and padlock design for in-situ sequencing
https://www.gear-genomics.com/
GNU General Public License v3.0
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Error with FM-Index #4

Closed Wentting closed 2 years ago

Wentting commented 2 years ago

I got an error with "FM-Index cannot be loaded!"

Here is my command

dicey search -c 45 -g Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz primers.fa -i /dicey/src/primer3_config/

I am not familar with C++, but i search for the error for a long time and i think there is somthing wrong with the genomeindex.json file. But I have load all the reference file from the recommend webset as following: fa.gz file, fa.gz.fai file, fa.gz.gzi file and the fa.fm9 file.

I really struggled with the error for many days, so it will be very appriciate for any advise!

Thank a ton!

tobiasrausch commented 2 years ago

Are you using the latest version of dicey?

dicey --version

Wentting commented 2 years ago

Thank you so much for your reply!

I am sure i am using the lastes version and all the FM-Indices files were all downloaded and put into one directiry from https://gear.embl.de/data/tracy/

Homo_sapiens.GRCh37.dna.primary_assembly.fa.fm9 Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz.fai Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz.gzi

I dont kown if these are all files I need. And, dicey I am using was pre-compiled version and downloaded from https://github.com/gear-genomics/dicey/releases

tobiasrausch commented 2 years ago

It should be 5 files for each genome build. I think you are missing Homo_sapiens.GRCh37.dna.primary_assembly.fa.fm9_check

Please download this file then it should work.

Wentting commented 2 years ago

I am so excited It works. Yes I should download the check file！

Thank you sooooooo much for your reply and your amazing work! Hope you have a nice day!