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griffithlab / pVACtools

http://www.pvactools.org
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FutureWarning: Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first #1067

Closed Stikus closed 6 months ago

Stikus commented 6 months ago

Installation Type

Standalone

pVACtools Version / Docker Image

4.0.8

Python Version

3.10

Operating System

Ubuntu 22.04

Describe the bug

Full warning message:

/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)

We've got several dozens of these messages per run.

Maybe related links:

How to reproduce this bug

python3 /usr/local/bin/pvacseq run -t 32 -e1 9,10 -e2 15 --pass-only  --iedb-install-directory /soft/IEDB /input/input.vcf TUMOR "HLA-A*02:01,HLA-B*35:01,DRB1*11:01" MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign /output

Input files

input.zip

Log output

[2024-02-20 13:16:33] [3/8] Running pVACtools ... pVACseq pipeline (len=9,10) ...
  Running using local IEDB ...
  Command: 'python3 /usr/local/bin/pvacseq run -t 32 -e1 9,10 -e2 15 --pass-only  --iedb-install-directory /soft/IEDB /input/input.vcf TUMOR "HLA-A*02:01,HLA-B*35:01,DRB1*11:01" MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign /output'.
  PID=244 (last job)
Executing MHC Class I predictions
Converting .vcf to TSV
/usr/local/lib/python3.10/dist-packages/vcfpy/header.py:284: DuplicateHeaderLineWarning: Seen FILTER header more than once: PASS, using firstoccurence
  warnings.warn(
Warning: Mismatch between the number of alternate alleles and number of values in the AD field for genotype Call('H_NJ-HCC1395-HCC1395', {'GT': '2/2', 'DP': 4, 'DP4': [0, 0, 2, 2], 'BQ': [33], 'SS': 2, 'AD': [0], 'DP2': 4, 'TAR': [0, 0], 'TIR': [6, 6], 'TOR': [0, 0], 'DP50': 5.73, 'FDP50': 0.34, 'SUBDP50': 0.0, 'FT': ['PASS']})
Completed
Converting VCF to TSV
Warning: Mismatch between the number of alternate alleles and number of values in the AD field for genotype Call('H_NJ-HCC1395-HCC1395', {'GT': '2/2', 'DP': 4, 'DP4': [0, 0, 2, 2], 'BQ': [33], 'SS': 2, 'AD': [0], 'DP2': 4, 'TAR': [0, 0], 'TIR': [6, 6], 'TOR': [0, 0], 'DP50': 5.73, 'FDP50': 0.34, 'SUBDP50': 0.0, 'FT': ['PASS']})
Completed
Generating Variant Peptide FASTA and Key File
Completed
Parsing the Variant Peptide FASTA and Key File
Completed
Calculating Manufacturability Metrics
Completed
Splitting TSV into smaller chunks
Splitting TSV into smaller chunks - Entries 1-24
Completed
Generating Variant Peptide FASTA and Key Files
Generating Variant Peptide FASTA and Key Files - Epitope Length 9 - Entries 1-48
Generating Variant Peptide FASTA and Key Files - Epitope Length 10 - Entries 1-48
Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/TUMOR.MHCnuggetsI.HLA-A*02:01.9.tsv_1-48
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHC - File /output/MHC_Class_I/tmp/TUMOR.ann.HLA-A*02:01.9.tsv_1-48
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method PickPocket - File /output/MHC_Class_I/tmp/TUMOR.pickpocket.HLA-A*02:01.9.tsv_1-48
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMM - File /output/MHC_Class_I/tmp/TUMOR.smm.HLA-A*02:01.9.tsv_1-48
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/TUMOR.smmpmbec.HLA-A*02:01.9.tsv_1-48
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method MHCflurry - File /output/MHC_Class_I/tmp/TUMOR.MHCflurry.HLA-A*02:01.10.tsv_1-48
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/TUMOR.MHCnuggetsI.HLA-A*02:01.10.tsv_1-48
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method NetMHC - File /output/MHC_Class_I/tmp/TUMOR.ann.HLA-A*02:01.10.tsv_1-48
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method PickPocket - File /output/MHC_Class_I/tmp/TUMOR.pickpocket.HLA-A*02:01.10.tsv_1-48
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method SMM - File /output/MHC_Class_I/tmp/TUMOR.smm.HLA-A*02:01.10.tsv_1-48
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/TUMOR.smmpmbec.HLA-A*02:01.10.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCflurry - File /output/MHC_Class_I/tmp/TUMOR.MHCflurry.HLA-B*35:01.9.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/TUMOR.MHCnuggetsI.HLA-B*35:01.9.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHC - File /output/MHC_Class_I/tmp/TUMOR.ann.HLA-B*35:01.9.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method PickPocket - File /output/MHC_Class_I/tmp/TUMOR.pickpocket.HLA-B*35:01.9.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMM - File /output/MHC_Class_I/tmp/TUMOR.smm.HLA-B*35:01.9.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/TUMOR.smmpmbec.HLA-B*35:01.9.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method MHCflurry - File /output/MHC_Class_I/tmp/TUMOR.MHCflurry.HLA-B*35:01.10.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/TUMOR.MHCnuggetsI.HLA-B*35:01.10.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method NetMHC - File /output/MHC_Class_I/tmp/TUMOR.ann.HLA-B*35:01.10.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method PickPocket - File /output/MHC_Class_I/tmp/TUMOR.pickpocket.HLA-B*35:01.10.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method SMM - File /output/MHC_Class_I/tmp/TUMOR.smm.HLA-B*35:01.10.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/TUMOR.smmpmbec.HLA-B*35:01.10.tsv_1-48
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCflurry - File /output/MHC_Class_I/tmp/TUMOR.MHCflurry.HLA-A*02:01.9.tsv_1-48
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method SMM - File /output/MHC_Class_I/tmp/TUMOR.smm.HLA-B*35:01.10.tsv_1-48 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMM - File /output/MHC_Class_I/tmp/TUMOR.smm.HLA-A*02:01.9.tsv_1-48 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/TUMOR.smmpmbec.HLA-A*02:01.10.tsv_1-48 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMM - File /output/MHC_Class_I/tmp/TUMOR.smm.HLA-B*35:01.9.tsv_1-48 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/TUMOR.smmpmbec.HLA-B*35:01.9.tsv_1-48 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/TUMOR.smmpmbec.HLA-A*02:01.9.tsv_1-48 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method SMM - File /output/MHC_Class_I/tmp/TUMOR.smm.HLA-A*02:01.10.tsv_1-48 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/TUMOR.smmpmbec.HLA-B*35:01.10.tsv_1-48 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHC - File /output/MHC_Class_I/tmp/TUMOR.ann.HLA-A*02:01.9.tsv_1-48 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHC - File /output/MHC_Class_I/tmp/TUMOR.ann.HLA-B*35:01.9.tsv_1-48 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method NetMHC - File /output/MHC_Class_I/tmp/TUMOR.ann.HLA-A*02:01.10.tsv_1-48 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method NetMHC - File /output/MHC_Class_I/tmp/TUMOR.ann.HLA-B*35:01.10.tsv_1-48 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/TUMOR.MHCnuggetsI.HLA-B*35:01.9.tsv_1-48 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/TUMOR.MHCnuggetsI.HLA-A*02:01.10.tsv_1-48 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/TUMOR.MHCnuggetsI.HLA-A*02:01.9.tsv_1-48 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/TUMOR.MHCnuggetsI.HLA-B*35:01.10.tsv_1-48 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method MHCflurry - File /output/MHC_Class_I/tmp/TUMOR.MHCflurry.HLA-B*35:01.10.tsv_1-48 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCflurry - File /output/MHC_Class_I/tmp/TUMOR.MHCflurry.HLA-A*02:01.9.tsv_1-48 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method MHCflurry - File /output/MHC_Class_I/tmp/TUMOR.MHCflurry.HLA-A*02:01.10.tsv_1-48 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCflurry - File /output/MHC_Class_I/tmp/TUMOR.MHCflurry.HLA-B*35:01.9.tsv_1-48 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method PickPocket - File /output/MHC_Class_I/tmp/TUMOR.pickpocket.HLA-B*35:01.10.tsv_1-48 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method PickPocket - File /output/MHC_Class_I/tmp/TUMOR.pickpocket.HLA-A*02:01.9.tsv_1-48 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method PickPocket - File /output/MHC_Class_I/tmp/TUMOR.pickpocket.HLA-B*35:01.9.tsv_1-48 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method PickPocket - File /output/MHC_Class_I/tmp/TUMOR.pickpocket.HLA-A*02:01.10.tsv_1-48 - Completed
Parsing prediction file for Allele HLA-A*02:01 and Epitope Length 9 - Entries 1-48
Parsing prediction file for Allele HLA-A*02:01 and Epitope Length 9 - Entries 1-48 - Completed
Parsing prediction file for Allele HLA-A*02:01 and Epitope Length 10 - Entries 1-48
Parsing prediction file for Allele HLA-A*02:01 and Epitope Length 10 - Entries 1-48 - Completed
Parsing prediction file for Allele HLA-B*35:01 and Epitope Length 9 - Entries 1-48
Parsing prediction file for Allele HLA-B*35:01 and Epitope Length 9 - Entries 1-48 - Completed
Parsing prediction file for Allele HLA-B*35:01 and Epitope Length 10 - Entries 1-48
Parsing prediction file for Allele HLA-B*35:01 and Epitope Length 10 - Entries 1-48 - Completed
Combining Parsed Prediction Files
Completed
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
Creating aggregated report
Tumor clonal VAF estimated as 0.5 (estimated from Tumor DNA VAF data). Assuming variants with VAF < 0.25 are subclonal
Completed
Calculating Manufacturability Metrics
Completed
Running Binding Filters
Completed
Running Coverage Filters
Completed
Running Transcript Support Level Filter
Complete
Running Top Score Filter
Completed

Done: Pipeline finished successfully. File /output/MHC_Class_I/TUMOR.filtered.tsv contains list of filtered putative neoantigens.

Executing MHC Class II predictions
Converting .vcf to TSV
/usr/local/lib/python3.10/dist-packages/vcfpy/header.py:284: DuplicateHeaderLineWarning: Seen FILTER header more than once: PASS, using firstoccurence
  warnings.warn(
Warning: Mismatch between the number of alternate alleles and number of values in the AD field for genotype Call('H_NJ-HCC1395-HCC1395', {'GT': '2/2', 'DP': 4, 'DP4': [0, 0, 2, 2], 'BQ': [33], 'SS': 2, 'AD': [0], 'DP2': 4, 'TAR': [0, 0], 'TIR': [6, 6], 'TOR': [0, 0], 'DP50': 5.73, 'FDP50': 0.34, 'SUBDP50': 0.0, 'FT': ['PASS']})
Completed
Converting VCF to TSV
Warning: Mismatch between the number of alternate alleles and number of values in the AD field for genotype Call('H_NJ-HCC1395-HCC1395', {'GT': '2/2', 'DP': 4, 'DP4': [0, 0, 2, 2], 'BQ': [33], 'SS': 2, 'AD': [0], 'DP2': 4, 'TAR': [0, 0], 'TIR': [6, 6], 'TOR': [0, 0], 'DP50': 5.73, 'FDP50': 0.34, 'SUBDP50': 0.0, 'FT': ['PASS']})
Completed
Generating Variant Peptide FASTA and Key File
Completed
Parsing the Variant Peptide FASTA and Key File
Completed
Calculating Manufacturability Metrics
Completed
Splitting TSV into smaller chunks
Splitting TSV into smaller chunks - Entries 1-24
Completed
Generating Variant Peptide FASTA and Key Files
Generating Variant Peptide FASTA and Key Files - Epitope Length 15 - Entries 1-48
Completed
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method NNalign - File /output/MHC_Class_II/tmp/TUMOR.nn_align.DRB1*11:01.15.tsv_1-48
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method SMMalign - File /output/MHC_Class_II/tmp/TUMOR.smm_align.DRB1*11:01.15.tsv_1-48
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method MHCnuggetsII - File /output/MHC_Class_II/tmp/TUMOR.MHCnuggetsII.DRB1*11:01.15.tsv_1-48
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method SMMalign - File /output/MHC_Class_II/tmp/TUMOR.smm_align.DRB1*11:01.15.tsv_1-48 - Completed
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method NNalign - File /output/MHC_Class_II/tmp/TUMOR.nn_align.DRB1*11:01.15.tsv_1-48 - Completed
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method MHCnuggetsII - File /output/MHC_Class_II/tmp/TUMOR.MHCnuggetsII.DRB1*11:01.15.tsv_1-48 - Completed
Parsing prediction file for Allele DRB1*11:01 and Epitope Length 15 - Entries 1-48
Parsing prediction file for Allele DRB1*11:01 and Epitope Length 15 - Entries 1-48 - Completed
Combining Parsed Prediction Files
Completed
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float32, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
/usr/local/lib/python3.10/dist-packages/pvactools/lib/aggregate_all_epitopes.py:322: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value 'NA' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  df.fillna(value="NA", inplace=True)
Creating aggregated report
Tumor clonal VAF estimated as 0.5 (estimated from Tumor DNA VAF data). Assuming variants with VAF < 0.25 are subclonal
Completed
Calculating Manufacturability Metrics
Completed
Running Binding Filters
Completed
Running Coverage Filters
Completed
Running Transcript Support Level Filter
Complete
Running Top Score Filter
Completed

Done: Pipeline finished successfully. File /output/MHC_Class_II/TUMOR.filtered.tsv contains list of filtered putative neoantigens.

Creating combined reports
Creating aggregated report
Tumor clonal VAF estimated as 0.5 (estimated from Tumor DNA VAF data). Assuming variants with VAF < 0.25 are subclonal
Completed
Running Binding Filters
Completed
Running Coverage Filters
Completed
Running Transcript Support Level Filter
Complete
Running Top Score Filter
Completed

Done: Pipeline finished successfully. File /output/combined/TUMOR.filtered.tsv contains list of filtered putative neoantigens.

Output files

No response

susannasiebert commented 6 months ago

I believe this issue was incidentally fixed as part of https://github.com/griffithlab/pVACtools/pull/1063 (commit b41cd01). It should go out with the next feature release.