medaka consensus step gets killed everytime

[an22an]

After creating a bam file with an assembly and an ONT Escherichia Dataset i want to create a consensus file with following command, which seem to always get killed no matter how large the file is. I am running medaka on a 16GB Ram device. Could it be a bug? Thank you!

medaka consensus Escherichia.contigs.il.bam.bam con.hdf --model r941_min_fast_g303 --batch 200 --threads 5

/// [14:37:34 - Predict] Reducing threads to 2, anymore is a waste. [14:37:34 - Predict] It looks like you are running medaka without a GPU and attempted to set a high number of threads. We have scaled this down to an optimal number. If you wish to improve performance please see https://nanoporetech.github.io/medaka/installation.html#improving-parallelism. [14:37:34 - Predict] Setting tensorflow inter/intra-op threads to 2/1. [14:37:34 - Predict] Processing region(s): C1_5206604:0-5206604 [14:37:34 - Predict] Using model: /usr/local/lib/python3.8/dist-packages/medaka/data/r941_min_fast_g303_model.hdf5. [14:37:34 - Predict] Processing 6 long region(s) with batching. [14:37:34 - MdlStore] filepath /usr/local/lib/python3.8/dist-packages/medaka/data/r941_min_fast_g303_model.hdf5 [14:37:35 - BAMFile] Creating pool of 16 BAM file sets. [14:37:35 - Sampler] Initializing sampler for consensus of region C1_5206604:0-1000000. [14:37:35 - Sampler] Initializing sampler for consensus of region C1_5206604:999000-1999000. [14:37:35 - PWorker] Running inference for 5.2M draft bases. [14:37:51 - Feature] Processed C1_5206604:999000.0-1998999.2 (median depth 280.0) [14:37:51 - Sampler] Took 16.24s to make features. [14:37:51 - Sampler] Initializing sampler for consensus of region C1_5206604:1998000-2998000. [14:37:52 - Feature] Processed C1_5206604:0.0-999999.5 (median depth 308.0) [14:37:52 - Sampler] Took 16.53s to make features. [14:37:52 - Sampler] Initializing sampler for consensus of region C1_5206604:2997000-3997000. [14:38:07 - Feature] Processed C1_5206604:1998000.0-2997999.5 (median depth 285.0) [14:38:07 - Sampler] Took 15.80s to make features. [14:38:07 - Sampler] Initializing sampler for consensus of region C1_5206604:3996000-4996000. Killed ///

Describe the bug A clear and concise description of what the bug is including the command that you have run.

Logging Please attach any relevant logging messages. (Use ``` before and after code blocks).

Environment (if you do not have a GPU, write No GPU):

• Installation method: docker image
• OS: [e.g. Ubuntu 16.04]
• medaka version: medaka 1.6.1
• GPU model: no gpu

[cjw85]

Hi @an22an,

You haven't mentioned on which OS you are running.

I note that you saying you are running with Docker. It is possible that your docker configuration has limited the resource that you can use. Are you using Docker Desktop? The preferences dialog has options for setting the maximum amount of CPU and memory available to docker.