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kapsakcj / nanoporeWorkflow

:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers
MIT License
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update to latest guppy version #38

Closed kapsakcj closed 3 years ago

kapsakcj commented 3 years ago

This is the latest module available as of today guppy/4.4.0

kapsakcj commented 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

kapsakcj commented 3 years ago

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

kapsakcj commented 3 years ago

^ 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

kapsakcj commented 3 years ago

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
kapsakcj commented 3 years ago

see nanoporetech/medaka issue 249 for more info

kapsakcj commented 3 years ago

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

kapsakcj commented 3 years ago

docker image for medaka 1.2.0 works fine in singularity. safe to migrate to this latest version

kapsakcj commented 3 years ago

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

kapsakcj commented 3 years ago

Runs fine on full sequencing runs. Closing....until yet another Guppy version is released