NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.
https://www.earthbiogenome.org/
GNU General Public License v3.0
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No ToLID for my species #107

Closed Estel-Kitsune closed 3 weeks ago

Estel-Kitsune commented 4 weeks ago

Apparently my species of interest Alauda arvensis and Panurus biarmicus (not from ERGA/BGE) do not have a ToLID :(

This is for A. arvensis:

WARN: Cannot serialize context map. Cause: null -- Resume will not work on this process
ERROR ~ Error executing process > 'ASSEMBLY_REPORT:REPORT_DTOL ()'

Caused by:
  Cannot invoke method getAt() on null object -- Check script '/cfs/klemming/home/e/estell/.nextflow/assets/NBISweden/Earth-Biogenome-Project-pilot/modules/local/report/dtol.nf' at line: 16

Source block:
  def tol_table = [
      tolId: tol_search_json.species[0].tolIds[0].tolId,
      species: tol_search_json.species[0].scientificName,
      class: tol_search_json.species[0].taxaClass,
      order: tol_search_json.species[0].order
  ].collect { key, value -> "$key\t$value" }.join('\n')
  file("$task.workDir/DToL.tsv").text = tol_table

From the .log

Jun-06 09:21:06.440 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: ASSEMBLY_REPORT:REPORT_DTOL (); status: COMPLETED; exit: -; error: java.lang.NullPointerException: Cannot get property 'tolId' on null object; workDir: /cfs/klemming/projects/supr/snic2020-2-25/nbis/assemblies/male_skylark/analyses/01_assembly-workflow_initial-run_rackham/work/dc/f75cd1eb85c240bd0e486f34a059d0]

Jun-06 09:21:06.436 [Actor Thread 253] DEBUG nextflow.processor.TaskContext - Failed to serialize delegate map items: [ 
  'taxid':[java.lang.Integer] = 88112
  '$':[java.lang.Boolean] = true
  'task':[nextflow.processor.TaskConfig] =
[...]
'json':[null] = [species:[[commonName:Eurasian skylark, currentHighestTolidNumber:0, family:Alaudidae, genus:Alauda, kingdom:Metazoa, order:Passeriformes, phylum:Chordata, prefix:bAlaArv, scientificName:Alauda arvensis, taxaClass:Aves, taxonomyId:88112, tolIds:[]]], totalNumSpecies:1]
]

Is ToLID only needed for reporting? Can it be an optional field?