Closed kapsakcj closed 3 years ago
actually latest available is guppy/4.4.1 , but it doesn't work due to NVIDIA drivers and CUDA versions being too old.
Might have to drop down to guppy/4.2.2 to get it to run smoothly until SCBS can update drivers
Guppy/4.4.1 module works now.
BUT. I will need to make medaka models match the latest guppy versions before I push this change
^ updating to latest medaka means making my own container of medaka (had trouble last time I tried this due to git LFS) or use the biocontainers docker image
for medaka 1.2.0, the model file with the highest guppy version is r941_min_high_g360
there is nothing for guppy 4.4.1
All models available:
Available:
r103_min_high_g345
r103_min_high_g360,
r103_prom_high_g360,
r103_prom_snp_g3210,
r103_prom_variant_g3210,
r10_min_high_g303,
r10_min_high_g340,
r941_min_fast_g303,
r941_min_high_g303,
r941_min_high_g330,
r941_min_high_g340_rle,
r941_min_high_g344,
r941_min_high_g351,
r941_min_high_g360,
r941_prom_fast_g303,
r941_prom_high_g303,
r941_prom_high_g330,
r941_prom_high_g344,
r941_prom_high_g360,
r941_prom_high_g4011,
r941_prom_snp_g303,
r941_prom_snp_g322,
r941_prom_snp_g360,
r941_prom_variant_g303, \
r941_prom_variant_g322,
r941_prom_variant_g360
Default consensus: r941_min_high_g360
Default snp: r941_prom_snp_g360
Default variant: r941_prom_variant_g360
see nanoporetech/medaka issue 249 for more info
oh lol, I already made a docker image for medaka 1.2.0. Need to test, make sure it works, before asking SCBS/Nishant to copy the docker image to their repository of sif's on the cluster
docker image for medaka 1.2.0 works fine in singularity. safe to migrate to this latest version
upgraded to guppy 4.4.2 (latest guppy release version as of today) in https://github.com/kapsakcj/nanoporeWorkflow/commit/1998471b44f34de0537839f9877d422c70a911e3
upgraded to medaka 1.2.0 in this commit: https://github.com/kapsakcj/nanoporeWorkflow/commit/5742c4514d27a1d2ababedb7b921cff7f008a48f
Still not going to close this issue until I've tested full sequencing runs with these changes
Runs fine on full sequencing runs. Closing....until yet another Guppy version is released
This is the latest module available as of today
guppy/4.4.0