Failed to run medaka consensus

[mazzalab]

Description of the bug

I am analyzing a single sample (fastq.gz file size ~140 GBytes) leaving the variant caller to the default (medaka).
It stops with an error: "Failed to run medaka consensus" (see below).
No idea where this error comes from. pepper-margin-deepvariant works, instead.

Command used and terminal output

nextflow run nf-core/nanoseq -r 3.1.0 -profile docker -params-file nf-params.json -c custom_params

where **nf-params.json**:
{
    "protocol": "DNA",
    "outdir": ".\/results",
    "call_variants": true,
    "input": "samplesheet.csv",
    "skip_demultiplexing": true,
    "call_variants": true,
    "skip_quantification": true,
    "skip_fusion_analysis": true,
    "skip_modification_analysis": true,
    "max_time": "20.h"
}

-----

OUTPUT:

ERROR ~ Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_VARIANT (sample_R1)'

Caused by:
  Process `NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_VARIANT (sample_R1)` terminated with an error exit status (1)


Command executed:

  medaka_variant \
      -d \
      -f genome.fa \
      -i sample_R1.sorted.bam \
      -o sample_R1 \
      -t 12 \
       \


  cat <<-END_VERSIONS > versions.yml
  "NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_VARIANT":
      medaka: $( medaka --version 2>&1 | sed 's/medaka //g' )
  END_VERSIONS

Command exit status:
  1

Command output:

  ++ Preparing data
  - Checking program versions
  Program    Version    Required   Pass
  bcftools   1.12       1.11       True
  bgzip      1.12       1.11       True
  minimap2   2.22       2.11       True
  samtools   1.12       1.11       True
  tabix      1.12       1.11       True

  ++ Running first pass to haplotag reads.
  + Running consensus calling
  - Running medaka consensus with /data/runs/2024-06-07/GM23-14050/20240607_1642_1B_PAW01711_387c256b/bfx/work/92/cdf710fd37f3ddd905a51d057c3e2d/sample_R1.sorted.bam --model r941_prom_hac_snp_g507
  * Failed to run medaka consensus.

Command error:
  [15:37:15 - Feature] Processed chr11:108891000.0-109890999.0 (median depth 44.0)
  [15:37:15 - Sampler] Took 0.95s to make features.
  [15:37:15 - Sampler] Initializing sampler for consensus of region chr11:110889000-111889000.
  [15:37:16 - Feature] Processed chr11:109890000.0-110889999.0 (median depth 43.0)
  [15:37:16 - Sampler] Took 0.95s to make features.
  [15:37:16 - Sampler] Initializing sampler for consensus of region chr11:111888000-112888000.
  [15:37:16 - Feature] Processed chr11:110889000.0-111888999.0 (median depth 42.0)
  [15:37:16 - Sampler] Took 0.96s to make features.
  [15:37:16 - Sampler] Initializing sampler for consensus of region chr11:112887000-113887000.
  [15:37:17 - Feature] Processed chr11:111888000.0-112887999.1 (median depth 44.0)
  [15:37:17 - Sampler] Took 0.96s to make features.
  [15:37:17 - Sampler] Initializing sampler for consensus of region chr11:113886000-114886000.
  [15:37:17 - Feature] Processed chr11:112887000.0-113886999.0 (median depth 42.0)
  [15:37:17 - Sampler] Took 0.97s to make features.
  [15:37:17 - Sampler] Initializing sampler for consensus of region chr11:114885000-115885000.
  [15:37:17 - PWorker] Batches in cache: 2333.
  [15:37:17 - PWorker] 4.5% Done (140.0/3103.0 Mbases) in 1721.7s
  [15:37:20 - Feature] Processed chr11:113886000.0-114885999.0 (median depth 43.0)
  [15:37:20 - Sampler] Took 3.81s to make features.
  [15:37:21 - Feature] Processed chr11:114885000.0-115884999.0 (median depth 43.0)
  [15:37:21 - Sampler] Took 3.96s to make features.
  [15:37:21 - Sampler] Initializing sampler for consensus of region chr11:115884000-116884000.
  [15:37:21 - Sampler] Initializing sampler for consensus of region chr11:116883000-117883000.
  [15:37:22 - Feature] Processed chr11:116883000.0-117882999.3 (median depth 41.0)
  [15:37:22 - Sampler] Took 1.14s to make features.
  [15:37:22 - Sampler] Initializing sampler for consensus of region chr11:117882000-118882000.
  [15:37:22 - Feature] Processed chr11:115884000.0-116883999.0 (median depth 43.0)
  [15:37:22 - Sampler] Took 1.22s to make features.
  [15:37:22 - Sampler] Initializing sampler for consensus of region chr11:118881000-119881000.
  [15:37:23 - Feature] Processed chr11:117882000.0-118881999.0 (median depth 41.0)
  [15:37:23 - Sampler] Took 1.03s to make features.
  [15:37:23 - Feature] Processed chr11:118881000.0-119880999.0 (median depth 40.0)
  [15:37:23 - Sampler] Initializing sampler for consensus of region chr11:119880000-120880000.
  [15:37:23 - Sampler] Took 0.96s to make features.
  [15:37:23 - Sampler] Initializing sampler for consensus of region chr11:120879000-121879000.
  [15:37:24 - Feature] Processed chr11:120879000.0-121878999.0 (median depth 43.0)
  [15:37:24 - Sampler] Took 0.97s to make features.
  [15:37:24 - Sampler] Initializing sampler for consensus of region chr11:121878000-122878000.
  [15:37:24 - Feature] Processed chr11:119880000.0-120879999.0 (median depth 43.0)
  [15:37:24 - Sampler] Took 1.01s to make features.
  [15:37:24 - Sampler] Initializing sampler for consensus of region chr11:122877000-123877000.
  [15:37:25 - Feature] Processed chr11:121878000.0-122877999.0 (median depth 43.0)
  [15:37:25 - Sampler] Took 1.21s to make features.
  [15:37:25 - Sampler] Initializing sampler for consensus of region chr11:123876000-124876000.
  [15:37:25 - Feature] Processed chr11:122877000.0-123876999.0 (median depth 41.0)
  [15:37:25 - Sampler] Took 1.23s to make features.
  [15:37:25 - Sampler] Initializing sampler for consensus of region chr11:124875000-125875000.
  [15:37:26 - PWorker] Batches in cache: 2346.
  /usr/local/bin/medaka_variant: line 136:   749 Killed                  medaka consensus "${BAM}" "${PROBS}" --model "${MEDAKAMODEL}" --batch_size "${BATCH_SIZE}" ${REG_OPT} --threads "${THREADS}" ${EXTRAOPTS}
  * Failed to run medaka consensus.

Relevant files

No response

System information

NF ver: 24.04.4.5917
Hardware: HPC
Executor: local
Container: Docker
OS: Ubuntu
nf-core/nanoseq ver: 3.1.0