Closed Estel-Kitsune closed 3 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?
Apparently my species of interest Alauda arvensis and Panurus biarmicus (not from ERGA/BGE) do not have a ToLID :(
This is for A. arvensis:
From the .log
Is ToLID only needed for reporting? Can it be an optional field?