no basecall model information in input data

[arecto0]

Operating System

Windows 10

Other Linux

No response

Workflow Version

v1.1.2

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

v5.1.14

CLI command run

No response

Workflow Execution - CLI Execution Profile

custom

What happened?

After updating from wf-amplicon v1.1.0 to v1.1.2, the workflow stops with error stating that no basecall model information is found in the input data for certain barcode. When repeating the wf on the same data, same error is reported for another barcode. 2 workflow logs provided as example. My input fastq files are generated in MinKNOW by re-basecalling with superior basecalling the pod5 that were generated on a mk1C (during the run I use fast basecalling as advised by ONT support) Example of a fastq is attached as txt, since I could not upload fastq file type. I did not have this error when using wf-amplicon v1.1.0. fastq_runid_270357d61291597a25b7ba1cb68aa9105133d817_0_0.txt

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/mnt/d/epi2melabs/workflows/epi2me-labs/wf-amplicon/main.nf` [sharp_beaver] DSL2 - revision: 7b8dda5f6f
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-amplicon v1.1.2
--------------------------------------------------------------------------------
Core Nextflow options
  runName                : sharp_beaver
  containerEngine        : docker
  launchDir              : /mnt/d/epi2melabs/instances/wf-amplicon_01J49499ZA7FEF7GDTZTACRN8T
  workDir                : /mnt/d/epi2melabs/instances/wf-amplicon_01J49499ZA7FEF7GDTZTACRN8T/work
  projectDir             : /mnt/d/epi2melabs/workflows/epi2me-labs/wf-amplicon
  userName               : epi2mewsl
  profile                : standard
  configFiles            : /mnt/d/epi2melabs/workflows/epi2me-labs/wf-amplicon/nextflow.config
Input Options
  fastq                  : /mnt/d/rsv20240710/analysis/MinKNOWbasecallingSUP/pass
  reads_downsampling_size: 0
  reference              : /mnt/d/RSV20240730_31_combined data/analysis/refseq_HRSVB_lineageBD41_CG.fasta
Pre-processing Options
  min_read_length        : 200
  drop_frac_longest_reads: 0
Output Options
  out_dir                : /mnt/d/epi2melabs/instances/wf-amplicon_01J49499ZA7FEF7GDTZTACRN8T/output
Advanced Options
  number_depth_windows   : 200
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-amplicon for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-amplicon v1.1.2.
--------------------------------------------------------------------------------
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
[83/f767a0] Submitted process > pipeline:variantCallingPipeline:sanitizeRefFile
[0a/87c97e] Submitted process > pipeline:getVersions
[92/95444a] Submitted process > fastcat (2)
[a7/124b84] Submitted process > pipeline:getParams
[61/3eb40f] Submitted process > fastcat (1)
[03/2da022] Submitted process > fastcat (3)
[e1/bca1f4] Submitted process > fastcat (4)
[ae/f8eb7c] Submitted process > fastcat (5)
[4e/fb9ae1] Submitted process > fastcat (6)
[b3/10ad76] Submitted process > fastcat (7)
[05/bcb6a1] Submitted process > fastcat (8)
[66/e0fad9] Submitted process > fastcat (9)
[c5/a29e74] Submitted process > pipeline:subsetReads (1)
[e0/a96128] Submitted process > pipeline:subsetReads (2)
[88/bf6777] Submitted process > fastcat (10)
[c8/4e6e07] Submitted process > fastcat (11)
[92/d91dbe] Submitted process > pipeline:subsetReads (3)
[fa/2fea5b] Submitted process > fastcat (12)
[a9/4ea0ab] Submitted process > fastcat (13)
[d2/94e935] Submitted process > fastcat (14)
[1d/44c8bf] Submitted process > fastcat (15)
[a8/2508b9] Submitted process > fastcat (16)
[3e/34068d] Submitted process > fastcat (17)
[20/6644ac] Submitted process > fastcat (18)
[4a/d1ec76] Submitted process > fastcat (19)
[dc/cc8ae4] Submitted process > fastcat (20)
[ff/b8cf59] Submitted process > pipeline:subsetReads (4)
[b2/287441] Submitted process > pipeline:subsetReads (5)
[f0/608e3c] Submitted process > pipeline:subsetReads (6)
[4d/850222] Submitted process > pipeline:subsetReads (7)
[6c/fe686a] Submitted process > pipeline:subsetReads (8)
[66/92d8eb] Submitted process > pipeline:subsetReads (9)
[91/943969] Submitted process > pipeline:subsetReads (10)
[9c/7c074b] Submitted process > pipeline:subsetReads (11)
[53/f9c066] Submitted process > pipeline:subsetReads (12)
[e3/a67fc7] Submitted process > pipeline:subsetReads (13)
[97/0b31d9] Submitted process > pipeline:subsetReads (14)
[b1/3257a3] Submitted process > pipeline:porechop (1)
[c8/54fd62] Submitted process > pipeline:addMedakaToVersionsFile
[40/3dd7d2] Submitted process > pipeline:subsetReads (15)
[bd/867e85] Submitted process > pipeline:subsetReads (16)
[4e/14a97c] Submitted process > pipeline:subsetReads (17)
[13/87be44] Submitted process > pipeline:porechop (2)
[ea/54eec6] Submitted process > pipeline:porechop (3)
[b2/c1fa02] Submitted process > pipeline:subsetReads (18)
[d0/7bdac2] Submitted process > pipeline:subsetReads (19)
[58/534a6b] Submitted process > pipeline:subsetReads (20)
[41/ebfdb7] Submitted process > pipeline:porechop (4)
[31/188b15] Submitted process > pipeline:porechop (5)
[3a/2e7140] Submitted process > pipeline:porechop (6)
[5f/95c9d0] Submitted process > pipeline:porechop (7)
[d0/d2674d] Submitted process > pipeline:porechop (8)
[dc/b0be66] Submitted process > pipeline:porechop (9)
[24/643e0b] Submitted process > pipeline:porechop (10)
[7d/995452] Submitted process > pipeline:porechop (11)
[cc/c6cf6e] Submitted process > pipeline:porechop (12)
[ea/119502] Submitted process > pipeline:porechop (13)
[33/ebf992] Submitted process > pipeline:porechop (14)
[94/903c0d] Submitted process > pipeline:porechop (15)
[60/55a0b5] Submitted process > pipeline:porechop (16)
[cd/f3ea0e] Submitted process > pipeline:porechop (17)
[8b/c6f66e] Submitted process > pipeline:porechop (18)
[5d/817920] Submitted process > pipeline:porechop (19)
[a8/7f3f85] Submitted process > pipeline:porechop (20)
[f0/7c9fa7] Submitted process > pipeline:variantCallingPipeline:alignReads (8)
[b2/d49c4c] Submitted process > pipeline:variantCallingPipeline:alignReads (12)
[c8/4df9f0] Submitted process > pipeline:variantCallingPipeline:alignReads (17)
[31/7453bb] Submitted process > pipeline:variantCallingPipeline:alignReads (2)
[4c/d4f31a] Submitted process > pipeline:variantCallingPipeline:alignReads (14)
[9f/a26fe6] Submitted process > pipeline:variantCallingPipeline:alignReads (9)
[65/69acd1] Submitted process > pipeline:variantCallingPipeline:alignReads (7)
[43/1e77f1] Submitted process > pipeline:variantCallingPipeline:alignReads (6)
[d6/442f0d] Submitted process > pipeline:variantCallingPipeline:alignReads (3)
[1e/f07a8d] Submitted process > pipeline:variantCallingPipeline:alignReads (16)
[51/d0dae9] Submitted process > pipeline:variantCallingPipeline:alignReads (10)
[51/c3c007] Submitted process > pipeline:variantCallingPipeline:alignReads (1)
[8d/ef535c] Submitted process > pipeline:variantCallingPipeline:alignReads (4)
[56/f911bb] Submitted process > pipeline:variantCallingPipeline:alignReads (20)
[1a/ca8869] Submitted process > pipeline:variantCallingPipeline:alignReads (11)
[d7/6d0d23] Submitted process > pipeline:variantCallingPipeline:alignReads (5)
[49/926199] Submitted process > pipeline:variantCallingPipeline:alignReads (19)
[f4/4ac42f] Submitted process > pipeline:variantCallingPipeline:alignReads (18)
[11/4c7e2c] Submitted process > pipeline:variantCallingPipeline:alignReads (13)
[ba/bc7b2b] Submitted process > pipeline:variantCallingPipeline:alignReads (15)
[90/6b4087] Submitted process > pipeline:variantCallingPipeline:mosdepth (1)
[96/6a292c] Submitted process > pipeline:variantCallingPipeline:bamstats (1)
[c9/06ab21] Submitted process > pipeline:variantCallingPipeline:mosdepth (2)
[69/c428f1] Submitted process > pipeline:variantCallingPipeline:bamstats (2)
[46/894945] Submitted process > pipeline:variantCallingPipeline:bamstats (3)
[2e/b1e43f] Submitted process > pipeline:variantCallingPipeline:mosdepth (3)
[d7/ab12cd] Submitted process > pipeline:variantCallingPipeline:mosdepth (4)
[f1/84ea71] Submitted process > pipeline:variantCallingPipeline:bamstats (4)
[d2/ea50ca] Submitted process > pipeline:variantCallingPipeline:bamstats (5)
[1f/7f475a] Submitted process > pipeline:variantCallingPipeline:bamstats (6)
[67/3360f6] Submitted process > pipeline:variantCallingPipeline:mosdepth (5)
[6c/15d5b7] Submitted process > pipeline:variantCallingPipeline:mosdepth (6)
[41/99147f] Submitted process > pipeline:variantCallingPipeline:bamstats (7)
[ef/71e0a3] Submitted process > pipeline:variantCallingPipeline:mosdepth (7)
[21/959fa5] Submitted process > pipeline:variantCallingPipeline:bamstats (8)
[f8/fa8c1f] Submitted process > pipeline:variantCallingPipeline:mosdepth (8)
[97/9541a2] Submitted process > pipeline:variantCallingPipeline:bamstats (9)
[3e/b7f3c5] Submitted process > pipeline:variantCallingPipeline:bamstats (10)
[e4/94607e] Submitted process > pipeline:variantCallingPipeline:mosdepth (9)
[60/b58c9a] Submitted process > pipeline:variantCallingPipeline:mosdepth (10)
[d9/a2f738] Submitted process > pipeline:variantCallingPipeline:bamstats (11)
[f1/c7e550] Submitted process > pipeline:variantCallingPipeline:bamstats (12)
[c1/4b42bf] Submitted process > pipeline:variantCallingPipeline:bamstats (13)
[3b/4db6ef] Submitted process > pipeline:variantCallingPipeline:mosdepth (11)
[6e/09f804] Submitted process > pipeline:variantCallingPipeline:mosdepth (12)
[13/30b966] Submitted process > pipeline:variantCallingPipeline:bamstats (14)
[fa/124f67] Submitted process > pipeline:variantCallingPipeline:mosdepth (13)
[ae/86568a] Submitted process > pipeline:variantCallingPipeline:mosdepth (14)
[1f/065517] Submitted process > pipeline:variantCallingPipeline:bamstats (15)
[5d/a4a546] Submitted process > pipeline:variantCallingPipeline:bamstats (16)
[2b/04adf9] Submitted process > pipeline:variantCallingPipeline:mosdepth (15)
[ee/b3a2b8] Submitted process > pipeline:variantCallingPipeline:bamstats (17)
[eb/4811eb] Submitted process > pipeline:variantCallingPipeline:mosdepth (16)
[a8/dbc481] Submitted process > pipeline:variantCallingPipeline:bamstats (18)
[05/904bb0] Submitted process > pipeline:variantCallingPipeline:bamstats (19)
[48/9f8c75] Submitted process > pipeline:variantCallingPipeline:mosdepth (17)
[39/6949fc] Submitted process > pipeline:variantCallingPipeline:bamstats (20)
[9b/d82dbe] Submitted process > pipeline:variantCallingPipeline:mosdepth (18)
[3d/98b529] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (1)
[1a/badd3c] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (2)
[48/119122] Submitted process > pipeline:variantCallingPipeline:mosdepth (19)
[7d/86740f] Submitted process > pipeline:variantCallingPipeline:mosdepth (20)
[b2/eae047] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (3)
[6d/bb9ac3] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (4)
[8b/70c664] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (5)
[6e/9a304d] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (6)
[5a/e1b62d] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (7)
[32/b29314] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (8)
[85/537976] Submitted process > pipeline:variantCallingPipeline:concatMosdepthResultFiles (20)
ERROR ~ Error executing process > 'pipeline:variantCallingPipeline:medakaConsensus (1)'
Caused by:
  Found no basecall model information in the input data for sample 'barcode18'. Please provide it with the `--override_basecaller_cfg` parameter. -- Check script '/mnt/d/epi2melabs/workflows/epi2me-labs/wf-amplicon/./modules/local/./common.nf' at line: 104
Source block:
  String region_arg = region ? "--regions '$region'" : ""
  String basecall_model = params.override_basecaller_cfg ?: meta.basecall_models[0]
  if (!basecall_model) {
          error "Found no basecall model information in the input data for " + \
              "sample '$meta.alias'. Please provide it with the " + \
              "`--override_basecaller_cfg` parameter."
      }
  """
      medaka consensus input.bam consensus_probs.hdf \
          --threads $task.cpus $region_arg --model $basecall_model:$type
      """
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
 -- Check '/mnt/d/epi2melabs/instances/wf-amplicon_01J49499ZA7FEF7GDTZTACRN8T/nextflow.log' file for details
[2e/513b79] Submitted process > pipeline:variantCallingPipeline:concatMosdepthResultFiles (19)
WARN: Killing running tasks (9)

Invocation logs
2024-08-02T08:46Z │ Initialising
2024-08-02T08:46Z │ Reading launch data
2024-08-02T08:46Z │ Acquiring database record
2024-08-02T08:46Z │ Starting workflow invocation
2024-08-02T08:46Z │ Connecting to app via IPC
2024-08-02T08:46Z │ Awaiting weblog via HTTP on 52055
2024-08-02T08:46Z │ Launching nextflow subprocess
2024-08-02T08:46Z │ Uplink established to app
2024-08-02T08:53Z │ Subprocess closed
2024-08-02T08:53Z │ Exiting

N E X T F L O W  ~  version 23.04.2
Launching `/mnt/d/epi2melabs/workflows/epi2me-labs/wf-amplicon/main.nf` [focused_brattain] DSL2 - revision: 7b8dda5f6f
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-amplicon v1.1.2
--------------------------------------------------------------------------------
Core Nextflow options
  runName                : focused_brattain
  containerEngine        : docker
  launchDir              : /mnt/d/epi2melabs/instances/wf-amplicon_01J495CXXFKP4FEB30N2APBH6R
  workDir                : /mnt/d/epi2melabs/instances/wf-amplicon_01J495CXXFKP4FEB30N2APBH6R/work
  projectDir             : /mnt/d/epi2melabs/workflows/epi2me-labs/wf-amplicon
  userName               : epi2mewsl
  profile                : standard
  configFiles            : /mnt/d/epi2melabs/workflows/epi2me-labs/wf-amplicon/nextflow.config
Input Options
  fastq                  : /mnt/d/rsv20240710/analysis/MinKNOWbasecallingSUP/pass
  reads_downsampling_size: 0
  reference              : /mnt/d/RSV20240730_31_combined data/analysis/refseq_HRSVB_lineageBD41_CG.fasta
Pre-processing Options
  drop_frac_longest_reads: 0
Output Options
  out_dir                : /mnt/d/epi2melabs/instances/wf-amplicon_01J495CXXFKP4FEB30N2APBH6R/output
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-amplicon for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-amplicon v1.1.2.
--------------------------------------------------------------------------------
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
[fa/b8f801] Submitted process > fastcat (2)
[fb/d9e912] Submitted process > pipeline:getVersions
[58/a1b241] Submitted process > pipeline:getParams
[42/55258c] Submitted process > pipeline:variantCallingPipeline:sanitizeRefFile
[1f/c92963] Submitted process > fastcat (1)
[5f/447562] Submitted process > fastcat (3)
[33/2b83a2] Submitted process > fastcat (4)
[4d/b79ac6] Submitted process > fastcat (5)
[d5/11acb8] Submitted process > fastcat (6)
[a3/00ba53] Submitted process > fastcat (7)
[89/b15325] Submitted process > fastcat (8)
[fc/041f01] Submitted process > pipeline:subsetReads (1)
[47/468b0e] Submitted process > fastcat (9)
[80/34e832] Submitted process > fastcat (10)
[7d/9df632] Submitted process > pipeline:subsetReads (2)
[21/a679a2] Submitted process > fastcat (11)
[23/46884a] Submitted process > pipeline:subsetReads (3)
[1a/70fffa] Submitted process > fastcat (12)
[ca/cbb308] Submitted process > fastcat (13)
[fc/98c6ae] Submitted process > fastcat (14)
[f3/e449f7] Submitted process > fastcat (15)
[14/84be92] Submitted process > fastcat (16)
[f6/2a547b] Submitted process > fastcat (17)
[6a/5ae4c8] Submitted process > fastcat (18)
[29/c063a9] Submitted process > pipeline:subsetReads (4)
[26/35cebd] Submitted process > fastcat (19)
[d8/13d701] Submitted process > fastcat (20)
[37/5f52ee] Submitted process > pipeline:subsetReads (5)
[4f/88b3c3] Submitted process > pipeline:subsetReads (6)
[d1/d1a66d] Submitted process > pipeline:subsetReads (7)
[66/399910] Submitted process > pipeline:subsetReads (8)
[6c/c11083] Submitted process > pipeline:subsetReads (9)
[ee/f4e49f] Submitted process > pipeline:subsetReads (10)
[7f/8daf71] Submitted process > pipeline:subsetReads (11)
[62/de07c1] Submitted process > pipeline:subsetReads (12)
[1d/b298cc] Submitted process > pipeline:subsetReads (13)
[0a/c531f7] Submitted process > pipeline:subsetReads (14)
[d0/ce08bf] Submitted process > pipeline:porechop (1)
[8b/1a3100] Submitted process > pipeline:subsetReads (15)
[28/ac1a92] Submitted process > pipeline:porechop (2)
[e2/92c41b] Submitted process > pipeline:addMedakaToVersionsFile
[7d/acae09] Submitted process > pipeline:subsetReads (16)
[1f/b77d00] Submitted process > pipeline:subsetReads (17)
[f4/7afa99] Submitted process > pipeline:subsetReads (18)
[de/095f3e] Submitted process > pipeline:porechop (3)
[9e/793a8b] Submitted process > pipeline:subsetReads (19)
[b4/4ac353] Submitted process > pipeline:subsetReads (20)
[cf/5d90cf] Submitted process > pipeline:porechop (4)
[2c/55b3dc] Submitted process > pipeline:porechop (5)
[e9/9f3b00] Submitted process > pipeline:porechop (6)
[19/71e7d8] Submitted process > pipeline:porechop (7)
[91/455611] Submitted process > pipeline:porechop (8)
[9c/1a2ede] Submitted process > pipeline:porechop (9)
[d4/7b3f6d] Submitted process > pipeline:porechop (10)
[c4/05b84b] Submitted process > pipeline:porechop (11)
[be/91eaaf] Submitted process > pipeline:porechop (12)
[b1/999b7c] Submitted process > pipeline:porechop (13)
[dd/2b5c94] Submitted process > pipeline:porechop (14)
[ca/d633bf] Submitted process > pipeline:porechop (15)
[70/ada2c6] Submitted process > pipeline:porechop (16)
[f6/52c766] Submitted process > pipeline:porechop (17)
[9e/961f9a] Submitted process > pipeline:porechop (18)
[f6/bba67e] Submitted process > pipeline:porechop (19)
[d4/a8034b] Submitted process > pipeline:porechop (20)
[ec/5c1675] Submitted process > pipeline:variantCallingPipeline:alignReads (6)
[a3/3ed28e] Submitted process > pipeline:variantCallingPipeline:alignReads (5)
[6a/aa292e] Submitted process > pipeline:variantCallingPipeline:alignReads (17)
[14/23a909] Submitted process > pipeline:variantCallingPipeline:alignReads (8)
[fb/2d4d3d] Submitted process > pipeline:variantCallingPipeline:alignReads (10)
[19/0f5509] Submitted process > pipeline:variantCallingPipeline:alignReads (18)
[be/6b8edd] Submitted process > pipeline:variantCallingPipeline:alignReads (2)
[a1/fa6e3e] Submitted process > pipeline:variantCallingPipeline:alignReads (13)
[27/631b6f] Submitted process > pipeline:variantCallingPipeline:alignReads (9)
[0e/09bcc2] Submitted process > pipeline:variantCallingPipeline:alignReads (3)
[1c/bcef85] Submitted process > pipeline:variantCallingPipeline:alignReads (14)
[7b/b9ea2a] Submitted process > pipeline:variantCallingPipeline:alignReads (20)
[50/627dee] Submitted process > pipeline:variantCallingPipeline:alignReads (11)
[45/fbf972] Submitted process > pipeline:variantCallingPipeline:alignReads (16)
[a8/c2df93] Submitted process > pipeline:variantCallingPipeline:alignReads (15)
[ad/0195c2] Submitted process > pipeline:variantCallingPipeline:alignReads (4)
[15/9683f5] Submitted process > pipeline:variantCallingPipeline:alignReads (1)
[2a/0a8cbb] Submitted process > pipeline:variantCallingPipeline:alignReads (19)
[bd/d76845] Submitted process > pipeline:variantCallingPipeline:alignReads (7)
[1b/4e25b1] Submitted process > pipeline:variantCallingPipeline:alignReads (12)
[49/0a5511] Submitted process > pipeline:variantCallingPipeline:mosdepth (1)
[8a/cda2a1] Submitted process > pipeline:variantCallingPipeline:bamstats (1)
[49/085f95] Submitted process > pipeline:variantCallingPipeline:mosdepth (2)
[25/4a0b9f] Submitted process > pipeline:variantCallingPipeline:bamstats (2)
[2b/aed52b] Submitted process > pipeline:variantCallingPipeline:bamstats (3)
[04/d55512] Submitted process > pipeline:variantCallingPipeline:mosdepth (3)
[05/673791] Submitted process > pipeline:variantCallingPipeline:mosdepth (4)
[f2/b385a4] Submitted process > pipeline:variantCallingPipeline:bamstats (4)
[c0/cd8261] Submitted process > pipeline:variantCallingPipeline:bamstats (5)
[0d/4890a9] Submitted process > pipeline:variantCallingPipeline:bamstats (6)
[6f/35c2c4] Submitted process > pipeline:variantCallingPipeline:mosdepth (5)
[9a/fce428] Submitted process > pipeline:variantCallingPipeline:mosdepth (6)
[9b/4a7ef0] Submitted process > pipeline:variantCallingPipeline:mosdepth (7)
[53/abca0a] Submitted process > pipeline:variantCallingPipeline:bamstats (7)
[cd/033ab3] Submitted process > pipeline:variantCallingPipeline:bamstats (8)
[bf/ead93c] Submitted process > pipeline:variantCallingPipeline:mosdepth (8)
[fa/7bb0dc] Submitted process > pipeline:variantCallingPipeline:bamstats (9)
[b0/f6b33d] Submitted process > pipeline:variantCallingPipeline:bamstats (10)
[6c/cc475b] Submitted process > pipeline:variantCallingPipeline:mosdepth (9)
[cf/ffa68f] Submitted process > pipeline:variantCallingPipeline:mosdepth (10)
[3e/f10b68] Submitted process > pipeline:variantCallingPipeline:bamstats (11)
[0a/e4d8ff] Submitted process > pipeline:variantCallingPipeline:bamstats (12)
[33/ae7404] Submitted process > pipeline:variantCallingPipeline:bamstats (13)
[a9/dc42ea] Submitted process > pipeline:variantCallingPipeline:mosdepth (11)
[72/45a342] Submitted process > pipeline:variantCallingPipeline:mosdepth (12)
[df/ddefc2] Submitted process > pipeline:variantCallingPipeline:mosdepth (13)
[d2/3f46f8] Submitted process > pipeline:variantCallingPipeline:bamstats (14)
[fb/5c1ea7] Submitted process > pipeline:variantCallingPipeline:mosdepth (14)
[f6/0f791b] Submitted process > pipeline:variantCallingPipeline:bamstats (15)
[e7/65b088] Submitted process > pipeline:variantCallingPipeline:bamstats (16)
[03/858a71] Submitted process > pipeline:variantCallingPipeline:bamstats (17)
[24/954038] Submitted process > pipeline:variantCallingPipeline:mosdepth (15)
[cc/907c88] Submitted process > pipeline:variantCallingPipeline:mosdepth (16)
[c2/04db4a] Submitted process > pipeline:variantCallingPipeline:bamstats (18)
[32/3775ae] Submitted process > pipeline:variantCallingPipeline:bamstats (19)
[54/7450af] Submitted process > pipeline:variantCallingPipeline:bamstats (20)
[84/585ab7] Submitted process > pipeline:variantCallingPipeline:mosdepth (17)
[b9/9e99e1] Submitted process > pipeline:variantCallingPipeline:mosdepth (18)
[a5/df90ea] Submitted process > pipeline:variantCallingPipeline:mosdepth (19)
[83/ed9881] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (1)
[4a/49b2f8] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (2)
[5e/587557] Submitted process > pipeline:variantCallingPipeline:mosdepth (20)
[32/7db099] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (3)
[7e/82e8f9] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (4)
[f0/9fcc4d] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (5)
[10/a31f2f] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (6)
[4a/db1073] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (7)
[c0/f7a96f] Submitted process > pipeline:variantCallingPipeline:concatMosdepthResultFiles (20)
[ec/99ae5f] Submitted process > pipeline:variantCallingPipeline:concatMosdepthResultFiles (1)
[68/750fb7] Submitted process > pipeline:variantCallingPipeline:concatMosdepthResultFiles (2)
[ee/48a1cc] Submitted process > pipeline:variantCallingPipeline:downsampleBAMforMedaka (8)
ERROR ~ Error executing process > 'pipeline:variantCallingPipeline:medakaConsensus (1)'
Caused by:
  Found no basecall model information in the input data for sample 'barcode07'. Please provide it with the `--override_basecaller_cfg` parameter. -- Check script '/mnt/d/epi2melabs/workflows/epi2me-labs/wf-amplicon/./modules/local/./common.nf' at line: 104
Source block:
  String region_arg = region ? "--regions '$region'" : ""
  String basecall_model = params.override_basecaller_cfg ?: meta.basecall_models[0]
  if (!basecall_model) {
          error "Found no basecall model information in the input data for " + \
              "sample '$meta.alias'. Please provide it with the " + \
              "`--override_basecaller_cfg` parameter."
      }
  """
      medaka consensus input.bam consensus_probs.hdf \
          --threads $task.cpus $region_arg --model $basecall_model:$type
      """
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
 -- Check '/mnt/d/epi2melabs/instances/wf-amplicon_01J495CXXFKP4FEB30N2APBH6R/nextflow.log' file for details
WARN: Killing running tasks (10)
Invocation logs
2024-08-02T09:05Z │ Initialising
2024-08-02T09:05Z │ Reading launch data
2024-08-02T09:05Z │ Acquiring database record
2024-08-02T09:05Z │ Starting workflow invocation
2024-08-02T09:05Z │ Connecting to app via IPC
2024-08-02T09:05Z │ Awaiting weblog via HTTP on 52349
2024-08-02T09:05Z │ Launching nextflow subprocess
2024-08-02T09:05Z │ Uplink established to app
2024-08-02T09:12Z │ Subprocess closed
2024-08-02T09:12Z │ Exiting

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

[SamStudio8]

Found no basecall model information in the input data for sample 'barcode18'. Please provide it with the --override_basecaller_cfg parameter. -- Check script '/mnt/d/epi2melabs/workflows/epi2me-labs/wf-amplicon/./modules/local/./common.nf' at line: 104

You will need to provide the basecaller model that your data set was called with using the override_basecaller_cfg parameter. You can find this parameter in the "Advanced options" section of the workflow setup. You can select the model you used from the drop down list.