Starting tsv processing.
Processing 435 files
Processing: metadata_folder/316_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleTypeSub1:
  leaf: missing value
  root: missing value
  stem: missing value
IonizationSourceAndPolarity:
  not specified: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  not applicable: missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  not applicable: missing value
IGNORED:  ATTRIBUTE_SampleTypeSub1
IGNORED:  ATTRIBUTE_sample_type
IGNORED:  ATTRIBUTE_y
IGNORED:  ATRIBUTE_z
IGNORED:  ATTRIBUTE_x
IGNORED:  ATTRIBUTE_treatment
Number of rows removed due to not enough metadata: 0
Returning 96 rows!
Processing: metadata_folder/118_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  ML import: not available: missing value
SampleTypeSub1:
  ML import: not available: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
IonizationSourceAndPolarity:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
UBERONBodyPartName:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 0
Returning 219 rows!
Processing: metadata_folder/33_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  ML import: not available: missing value
SampleTypeSub1:
  ML import: not available: missing value
NCBITaxonomy:
  ML import: not available: missing value
YearOfAnalysis:
  1999: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
MassSpectrometer:
  ML import: not available: missing value
IonizationSourceAndPolarity:
  ML import: not available: missing value
ChromatographyAndPhase:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
UBERONBodyPartName:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 28
Returning 14 rows!
Processing: metadata_folder/245_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
TermsofPosition:
  not applicable: missing value
DOIDCommonName:
  Influenza Virus: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
Number of rows removed due to not enough metadata: 0
Returning 396 rows!
Processing: metadata_folder/303_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  ML import: not available: missing value
SampleTypeSub1:
  ML import: not available: missing value
NCBITaxonomy:
  ML import: not available: missing value
  114452|Bathymodiolus childressi: missing value
  not applicable: missing value
YearOfAnalysis:
  1999: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
MassSpectrometer:
  ML import: not available: missing value
IonizationSourceAndPolarity:
  ML import: not available: missing value
ChromatographyAndPhase:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
UBERONBodyPartName:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 2
Returning 13 rows!
Processing: metadata_folder/26_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  ML import: not available: missing value
SampleTypeSub1:
  ML import: not available: missing value
NCBITaxonomy:
  ML import: not available: missing value
YearOfAnalysis:
  1999: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
MassSpectrometer:
  ML import: not available: missing value
IonizationSourceAndPolarity:
  ML import: not available: missing value
ChromatographyAndPhase:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
UBERONBodyPartName:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 60
Returning 30 rows!
Processing: metadata_folder/250_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
MassSpectrometer:
  not specified: missing value
BiologicalSex:
  not specified: missing value
UBERONBodyPartName:
  not specified: missing value
TermsofPosition:
  not specified: missing value
HealthStatus:
  not specified: missing value
DOIDCommonName:
  not specified: missing value
ComorbidityListDOIDIndex:
  not specified: missing value
HumanPopulationDensity:
  not specified: missing value
LatitudeandLongitude:
  nan: missing value
Number of rows removed due to not enough metadata: 0
Returning 8 rows!
Processing: metadata_folder/408_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleTypeSub1:
  not applicable: missing value
NCBITaxonomy:
  135461|Bacillus subtilis: 135461|Bacillus subtilis subsp. subtilis
  : missing value
SampleExtractionMethod:
  not specified: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  not applicable: missing value
  : missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  not applicable: missing value
Number of rows removed due to not enough metadata: 0
Returning 2 rows!
Processing: metadata_folder/132_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleTypeSub1:
  ML import: not available: missing value
YearOfAnalysis:
  1999: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 0
Returning 240 rows!
Processing: metadata_folder/19_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  ML import: not available: missing value
SampleTypeSub1:
  ML import: not available: missing value
NCBITaxonomy:
  ML import: not available: missing value
YearOfAnalysis:
  1999: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
MassSpectrometer:
  ML import: not available: missing value
IonizationSourceAndPolarity:
  ML import: not available: missing value
ChromatographyAndPhase:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
UBERONBodyPartName:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 634
Returning 181 rows!
Processing: metadata_folder/381_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleTypeSub1:
  not specified: missing value
SampleExtractionMethod:
  not specified: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  nan: missing value
TermsofPosition:
  nan: missing value
HealthStatus:
  nan: missing value
DOIDCommonName:
  nan: missing value
ComorbidityListDOIDIndex:
  nan: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  nan: missing value
Number of rows removed due to not enough metadata: 0
Returning 8 rows!
Processing: metadata_folder/422_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleTypeSub1:
  not applicable: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  not applicable: missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  not applicable: missing value
IGNORED:  ATTRIBUTE_City
IGNORED:  ATTRIBUTE_Process
Number of rows removed due to not enough metadata: 0
Returning 17 rows!
Processing: metadata_folder/127_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  ML import: not available: missing value
SampleTypeSub1:
  ML import: not available: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
IonizationSourceAndPolarity:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 0
Returning 18 rows!
Processing: metadata_folder/394_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
NCBITaxonomy:
  535026|Bacillus subtilis: 535026|Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10
  2517241|Bacillus velezensis: 2517241|Bacillus velezensis A3
  451709|Bacillus cereus: 451709|Bacillus cereus 03BB108
  332648|Botrytis cinerea: 332648|Botrytis cinerea B05.10
  86192|Pseudomonas chlororaphis: 86192|Pseudomonas chlororaphis subsp. aurantiaca
  196023|Aeromonas hydrophila: 196023|Aeromonas hydrophila subsp. hydrophila
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  not applicable: missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
Number of rows removed due to not enough metadata: 0
Returning 39 rows!
Processing: metadata_folder/329_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
NCBITaxonomy:
  : missing value
  316385|E. coli strain K12: 316385|Escherichia coli str. K-12 substr. DH10B
  1506|Clostridium sp: 1506|Clostridium sp.
  502558|Eggerthella sp: 502558|Eggerthella sp. YY7918
  1384484|Adlercreutzia equolifaciens: 1384484|Adlercreutzia equolifaciens DSM 19450
  133561|Gordonibacter urolithinfaciens: 133561|Commersonia
  1532|Clostridium coccoides: 1532|Blautia coccoides
  622312|Roseburia inulinivorans: 622312|Roseburia inulinivorans DSM 16841
  585394|Roseburia hominis: 585394|Roseburia hominis A2-183
  411469|Eubacterium hallii: 411469|Anaerobutyricum hallii DSM 3353
  557436|Lactobacillus reuteri: 557436|Limosilactobacillus reuteri subsp. reuteri
  649753|Flavonifractor plautii: 649753|Flavonifractor plautii DSM 6740
  411459|Blautia obeum: 411459|Blautia obeum ATCC 29174
  1203554|Sutterella wadsworthensis: 1203554|Sutterella wadsworthensis HGA0223
  435590|Bacteroides vulgatus: 435590|Phocaeicola vulgatus ATCC 8482
  679935|Alistipes finegoldii: 679935|Alistipes finegoldii DSM 17242
  435591|Parabacteroides distasonis: 435591|Parabacteroides distasonis ATCC 8503
  349741|Akkermansia muciniphila: 349741|Akkermansia muciniphila ATCC BAA-835
  1150460|Bifidobacterium kashiwanohense: 1150460|Bifidobacterium catenulatum subsp. kashiwanohense JCM 15439 = DSM 21854
  391904|Bifidobacterium longum subsp. infantis: 391904|Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
  657308|Gordonibacter pamelaeae: 657308|Gordonibacter pamelaeae 7-10-1-b
SampleCollectionMethod:
  not applicable: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  : missing value
  not applicable: missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  not applicable: missing value
IGNORED:  ATTRIBUTE_sample_type
IGNORED:  ATTRIBUTE_incubationtime
IGNORED:  ATTRIBUTE_refchem
IGNORED:  ATTRIBUTE_NCBITaxonomy
Number of rows removed due to not enough metadata: 0
Returning 222 rows!
Processing: metadata_folder/106_gnps_metadata.tsv
qiita_sample_name: ADDED!
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
NCBITaxonomy:
  not applicable: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  not applicable: missing value
TermsofPosition:
  not applicable: missing value
DOIDCommonName:
  no disease reported: missing value
ComorbidityListDOIDIndex:
  not specified: missing value
LatitudeandLongitude:
  not specified: missing value
Number of rows removed due to not enough metadata: 0
Returning 65 rows!
Processing: metadata_folder/90_gnps_metadata.tsv
qiita_sample_name: ADDED!
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
TermsofPosition:
  not applicable: missing value
DOIDCommonName:
  no disease reported: missing value
ComorbidityListDOIDIndex:
  no disease reported: missing value
LatitudeandLongitude:
  not specified: missing value
Number of rows removed due to not enough metadata: 0
Returning 223 rows!
Processing: metadata_folder/403_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleTypeSub1:
  not applicable: missing value
NCBITaxonomy:
  135461|Bacillus subtilis: 135461|Bacillus subtilis subsp. subtilis
  : missing value
SampleExtractionMethod:
  not specified: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  not applicable: missing value
  : missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  not applicable: missing value
Number of rows removed due to not enough metadata: 0
Returning 2 rows!
Processing: metadata_folder/308_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  ML import: not available: missing value
SampleTypeSub1:
  ML import: not available: missing value
NCBITaxonomy:
  ML import: not available: missing value
YearOfAnalysis:
  1999: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
MassSpectrometer:
  ML import: not available: missing value
IonizationSourceAndPolarity:
  ML import: not available: missing value
ChromatographyAndPhase:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
UBERONBodyPartName:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 9
Returning 264 rows!
Processing: metadata_folder/38_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  ML import: not available: missing value
SampleTypeSub1:
  ML import: not available: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
IonizationSourceAndPolarity:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 0
Returning 44 rows!
Processing: metadata_folder/416_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleTypeSub1:
  not applicable: missing value
NCBITaxonomy:
  not applicable: missing value
  228215|Pleurotus eryngii ferulae: 228215|Pleurotus eryngii var. ferulae
  : missing value
SampleCollectionMethod:
  not applicable: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  not applicable: missing value
  : missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  not applicable: missing value
IGNORED:  ATTRIBUTE_Taxonomy
IGNORED:  SampleType1
IGNORED:  ATTRIBUTE_ Percent of OMSW
Number of rows removed due to not enough metadata: 0
Returning 61 rows!
Processing: metadata_folder/85_gnps_metadata.tsv
qiita_sample_name: ADDED!
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  not applicable: missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  not specified: missing value
Number of rows removed due to not enough metadata: 0
Returning 126 rows!
Processing: metadata_folder/113_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  ML import: not available: missing value
SampleTypeSub1:
  ML import: not available: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
MassSpectrometer:
  ML import: not available: missing value
IonizationSourceAndPolarity:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 0
Returning 393 rows!
Processing: metadata_folder/322_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
NCBITaxonomy:
  not applicable: missing value
  : missing value
  435590|Bacteroides vulgatus: 435590|Phocaeicola vulgatus ATCC 8482
  349741|Akkermansia muciniphila: 349741|Akkermansia muciniphila ATCC BAA-835
  391904|Bifidobacterium longum subsp. infantis: 391904|Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
SampleCollectionMethod:
  not applicable: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  not applicable: missing value
  : missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  not applicable: missing value
IGNORED:  ATTRIBUTE_chemmix
IGNORED:  ATTRIBUTE_incubationtime
IGNORED:  ATTRIBUTE_sample_type
IGNORED:  ATTRIBUTE_NCBITaxonomy
IGNORED:  ATTRIBUTE_coffee
Number of rows removed due to not enough metadata: 0
Returning 110 rows!
Processing: metadata_folder/191_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
NCBITaxonomy:
  not applicable: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  not applicable: missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
LatitudeandLongitude:
  -34.041176; 25.538640: missing value
IGNORED:  Sampling Location 
IGNORED:  linked_tissue_sample
IGNORED:  DOM_Filter_LOT_number
Number of rows removed due to not enough metadata: 0
Returning 44 rows!
Processing: metadata_folder/271_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  ML import: not available: missing value
SampleTypeSub1:
  ML import: not available: missing value
NCBITaxonomy:
  ML import: not available: missing value
YearOfAnalysis:
  1999: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
MassSpectrometer:
  ML import: not available: missing value
IonizationSourceAndPolarity:
  ML import: not available: missing value
ChromatographyAndPhase:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
UBERONBodyPartName:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 432
Returning 72 rows!
Processing: metadata_folder/337_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
NCBITaxonomy:
  : missing value
  1206781|Paenibacillus alvei: 1206781|Paenibacillus alvei DSM 29
  1087481|Paenibacillus peoriae: 1087481|Paenibacillus peoriae KCTC 3763
  not applicable: missing value
SampleCollectionMethod:
  not applicable: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  : missing value
  not applicable: missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  not applicable: missing value
IGNORED:  ATTRIBUTE_sample_type
IGNORED:  ATTRIBUTE_incubationtime
IGNORED:  ATTRIBUTE_NCBITaxonomy
Number of rows removed due to not enough metadata: 0
Returning 86 rows!
Processing: metadata_folder/184_gnps_metadata.tsv
qiita_sample_name: ADDED!
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
NCBITaxonomy:
  : missing value
SampleCollectionMethod:
  not applicable: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  : missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
  no disease reported: missing value
  disease NOS: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  32.842;-117.258: missing value
Number of rows removed due to not enough metadata: 0
Returning 93 rows!
Processing: metadata_folder/264_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  ML import: not available: missing value
SampleTypeSub1:
  ML import: not available: missing value
NCBITaxonomy:
  not applicable: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
MassSpectrometer:
  ML import: not available: missing value
IonizationSourceAndPolarity:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
UBERONBodyPartName:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 16
Returning 164 rows!
Processing: metadata_folder/139_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  ML import: not available: missing value
SampleTypeSub1:
  ML import: not available: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
IonizationSourceAndPolarity:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
UBERONBodyPartName:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
Number of rows removed due to not enough metadata: 0
Returning 24 rows!
Processing: metadata_folder/233_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
NCBITaxonomy:
  : missing value
SampleCollectionMethod:
  not applicable: missing value
SampleExtractionMethod:
  not specified: missing value
BiologicalSex:
  not applicable: missing value
  not collected: missing value
UBERONBodyPartName:
  : missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
  not collected: missing value
DOIDCommonName:
  not applicable: missing value
  not specified: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
  not specified: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  not applicable: missing value
Number of rows removed due to not enough metadata: 0
Returning 27 rows!
Processing: metadata_folder/45_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleTypeSub1:
  ML import: not available: missing value
SampleCollectionMethod:
  ML import: not available: missing value
SampleExtractionMethod:
  ML import: not available: missing value
InternalStandardsUsed:
  ML import: not available: missing value
BiologicalSex:
  ML import: not available: missing value
TermsofPosition:
  ML import: not available: missing value
HealthStatus:
  ML import: not available: missing value
DOIDCommonName:
  ML import: not available: missing value
ComorbidityListDOIDIndex:
  ML import: not available: missing value
Country:
  ML import: not available: missing value
HumanPopulationDensity:
  ML import: not available: missing value
LatitudeandLongitude:
  ML import: not available: missing value
IGNORED:  sample_name
IGNORED:  Unnamed: 0
Number of rows removed due to not enough metadata: 0
Returning 264 rows!
Processing: metadata_folder/360_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  not applicable: missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  nan: missing value
Number of rows removed due to not enough metadata: 0
Returning 96 rows!
Processing: metadata_folder/226_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
NCBITaxonomy:
  : missing value
  not specified|Staphylococcus aureus JE3: missing value
SampleCollectionMethod:
  not applicable: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  : missing value
  not applicable: missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  not applicable: missing value
IGNORED:  ATTRIBUTE_SampleType
Number of rows removed due to not enough metadata: 0
Returning 75 rows!
Processing: metadata_folder/50_gnps_metadata.tsv
qiita_sample_name: ADDED!
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
NCBITaxonomy:
  : missing value
  not applicable: missing value
SampleCollectionMethod:
  not applicable: missing value
SampleExtractionMethod:
  not specified: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  not specified: missing value
  : missing value
TermsofPosition:
  not applicable: missing value
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not specified: missing value
ComorbidityListDOIDIndex:
  not applicable: missing value
LatitudeandLongitude:
  not specified: missing value
Number of rows removed due to not enough metadata: 0
Returning 533 rows!
Processing: metadata_folder/MSV000079949.tsv
SampleTypeSub1: ADDED!
YearOfAnalysis: ADDED!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
IonizationSourceAndPolarity: ADDED!
ChromatographyAndPhase: ADDED!
SubjectIdentifierAsRecorded: ADDED!
TermsofPosition: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleType:
  blank: missing value
  QC: missing value
  tissue: missing value
  biofluid: missing value
NCBITaxonomy:
  : missing value
  QC: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  : missing value
  not applicable: missing value
  gall bladder: gallbladder
HealthStatus:
  not applicable: missing value
DOIDCommonName:
  not applicable: missing value
IGNORED:  Social_Economical_Status
IGNORED:  Ethnicity
IGNORED:  Cluster1
Number of rows removed due to not enough metadata: 61
Returning 773 rows!
Processing: metadata_folder/375_gnps_metadata.tsv
ENVOEnvironmentBiome: ADDED!
ENVOEnvironmentMaterial: ADDED!
SampleTypeSub1:
  not specified: missing value
SampleExtractionMethod:
  not specified: missing value
BiologicalSex:
  not applicable: missing value
UBERONBodyPartName:
  nan: missing value
TermsofPosition:
  nan: missing value
HealthStatus:
  nan: missing value
DOIDCommonName:
  nan: missing value
ComorbidityListDOIDIndex:
  nan: missing value
HumanPopulationDensity:
  not applicable: missing value
LatitudeandLongitude:
  nan: missing value
Number of rows removed due to not enough metadata: 0
Returning 8 rows!
Processing: metadata_folder/MSV000094560.tsv
NCBITaxonomy:
  : missing value
SampleExtractionMethod:
  Not Applicable: missing value
InternalStandardsUsed:
  biotin: missing value
MassSpectrometer:
  Orbitrap IQ-X|MS:1003411: missing value
ChromatographyAndPhase:
  reverse phase (porous graphitic carbon): missing value
BiologicalSex:
  Not Applicable: missing value
UBERONBodyPartName:
  : missing value
  Not Applicable: missing value
TermsofPosition:
  Not Applicable: missing value
HealthStatus:
  Not Applicable: missing value
DOIDCommonName:
  Not Applicable: missing value
ComorbidityListDOIDIndex:
  Not Applicable: missing value
HumanPopulationDensity:
  Not Applicable: missing value
LatitudeandLongitude:
  Not Applicable: missing value
ENVOEnvironmentBiome:
  Not Applicable: missing value
Traceback (most recent call last):
  File "/app/workflows/PublicDataset_ReDU_Metadata_Workflow/conda/conda_env-88e285eea3d03e468983bcd88c95c51f/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3653, in get_loc
    return self._engine.get_loc(casted_key)
  File "pandas/_libs/index.pyx", line 147, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 176, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 7080, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 7088, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'NCBIRank'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py", line 307, in <module>
    df = complete_and_fill_REDU_table(df, 
  File "/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py", line 194, in complete_and_fill_REDU_table
    df['NCBIRank'].fillna(missing_value, inplace=True)
  File "/app/workflows/PublicDataset_ReDU_Metadata_Workflow/conda/conda_env-88e285eea3d03e468983bcd88c95c51f/lib/python3.8/site-packages/pandas/core/frame.py", line 3761, in __getitem__
    indexer = self.columns.get_loc(key)
  File "/app/workflows/PublicDataset_ReDU_Metadata_Workflow/conda/conda_env-88e285eea3d03e468983bcd88c95c51f/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3655, in get_loc
    raise KeyError(key) from err
KeyError: 'NCBIRank'