Error running medaka_consensus

[RayanaFeltrin]

Hello!

I have installed medaka 1.8.1 using a virtual environment, as well as its dependencies, on an Ubuntu 20.04.4 LTS with no GPU. Then I have run the script below, following the model suggested in README:

#!/bin/bash

source medaka/bin/activate
NPROC=$(nproc)
BASECALLS=/home/rayana/Documents/Genomes_Nanopore/6set2022_4genomas/20220906_1853_MN19475_FAK88705_0a2345f8/fast5_guppy/pass/barcode11/*fastq
DRAFT=/home/rayana/Documents/Genomes_ONT_only/AM1001_ONT_contigs.fasta
OUTDIR=medaka_consensus

medaka_consensus -i ${BASECALLS} -d ${DRAFT} -o ${OUTDIR} -t ${NPROC} -m r104_min_sup_g642

So I got the following message:

medaka 1.8.1

Assembly polishing via neural networks. Medaka is optimized to work with the Flye assembler.

medaka_consensus [-h] -i -d

-h  show this help text.
-i  fastx input basecalls (required).
-d  fasta input assembly (required).
-o  output folder (default: medaka).
-g  don't fill gaps in consensus with draft sequence.
-r  use gap-filling character instead of draft sequence (default: None)
-m  medaka model, (default: r1041_e82_400bps_sup_v4.2.0).
    Choices: r103_fast_g507 r103_hac_g507 r103_min_high_g345 r103_min_high_g360 r103_prom_high_g360 r103_sup_g507 r1041_e82_260bps_fast_g632 r1041_e82_260bps_hac_g632 r1041_e82_260bps_hac_v4.0.0 r1041_e82_260bps_hac_v4.1.0 r1041_e82_260bps_sup_g632 r1041_e82_260bps_sup_v4.0.0 r1041_e82_260bps_sup_v4.1.0 r1041_e82_400bps_fast_g615 r1041_e82_400bps_fast_g632 r1041_e82_400bps_hac_g615 r1041_e82_400bps_hac_g632 r1041_e82_400bps_hac_v4.0.0 r1041_e82_400bps_hac_v4.1.0 r1041_e82_400bps_hac_v4.2.0 r1041_e82_400bps_sup_g615 r1041_e82_400bps_sup_v4.0.0 r1041_e82_400bps_sup_v4.1.0 r1041_e82_400bps_sup_v4.2.0 r104_e81_fast_g5015 r104_e81_hac_g5015 r104_e81_sup_g5015 r104_e81_sup_g610 r10_min_high_g303 r10_min_high_g340 r941_e81_fast_g514 r941_e81_hac_g514 r941_e81_sup_g514 r941_min_fast_g303 r941_min_fast_g507 r941_min_hac_g507 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_min_sup_g507 r941_prom_fast_g303 r941_prom_fast_g507 r941_prom_hac_g507 r941_prom_high_g303 r941_prom_high_g330 r941_prom_high_g344 r941_prom_high_g360 r941_prom_high_g4011 r941_prom_sup_g507 r941_sup_plant_g610
    Alternatively a .tar.gz/.hdf file from 'medaka train'.
-f  Force overwrite of outputs (default will reuse existing outputs).
-x  Force recreation of alignment index.
-t  number of threads with which to create features (default: 1).
-b  batchsize, controls memory use (default: 100).
-q  Output consensus with per-base quality scores (fastq).

-d must be specified.

After that, I have double checked the paths of BASECALLS and DRAFT and everything seems correct. However, I have realized that the model I chose (r104_min_sup_g642 => flowcell 10.4, MinION, Guppy 6.4.2 run in sup mode) is not available on the model list. So I randomly chose any model to run in order to check if this was the problem, but I've got the same error message. Is there anything I can do to try solving this problem? What model do you suggest for me to use?

Thank you in advance.

[RayanaFeltrin]

Hello!

I have solved part of the issue running the command inside the script directly in the terminal, like this: medaka_consensus -i /home/rayana/Documents/Genomes_Nanopore/6set2022_4genomas/20220906_1853_MN19475_FAK88705_0a2345f8/fast5_guppy/pass/barcode11/fastq_runid_353c5d5a3a4274b1ccc980f2669c44b1911efc64_15_0.fastq -d /home/rayana/Documents/Genomes_ONT_only/AM1001_ONT_contigs.fasta -o medaka_consensus -t $(nproc) -m r941_min_high_g303 (note that I have inputted only one fastq file and have also changed the model to default to make it work))

However, I still have the question: what model do you suggest for me to use based on flowcell 10.4, MinION, and Guppy 6.4.2 run in sup mode?

Thank you in advance.

[cjw85]

You should use r1041_e82_400bps_sup_g615:

https://github.com/nanoporetech/medaka/issues/442#issuecomment-1606999964

From the README.