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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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How long should indexing take? #6

Closed gtbil closed 1 year ago

gtbil commented 1 year ago

I'm trying to dicey index a 2.4Gb plant genome assembly. How long should I expect creating the FM-Index to take, roughly?

tobiasrausch commented 1 year ago

4-8 hours depending on the machine but you only need to do this once.

gtbil commented 1 year ago

OK, I might be experiencing an issue then. I'm running the precompiled binary v0.2.3 on an HPC (20 threads, 374GB memory) and its been going for 9 hours. I tried doing one chromosome (out of 26) and that one has been running for over 1h. Would you anticipate building from source or running the singularity version helping?

gtbil commented 1 year ago

It has now been 21 hours. The genome is available here: https://data.jgi.doe.gov/refine-download/phytozome?genome_id=698

tobiasrausch commented 1 year ago

I have sent you the index files via Aspera. Seems to work fine with:

dos2unix Coker312.fa bgzip Coker312.fa samtools faidx Coker312.fa.gz dicey index -o Coker312.fa.fm9 Coker312.fa.gz

gtbil commented 1 year ago

I ran dicey index on my local machine and it is now working. You can close the issue.