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griffithlab / pVACtools

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Error with MHCflurry and NetMHCcons Predictions in pvactools #1161

Open seetarajpara opened 4 days ago

seetarajpara commented 4 days ago

Hi, I’m encountering errors while running pvactools (version 4.4.1) on a SLURM-managed HPC cluster. The pipeline fails during MHC Class I predictions, specifically with NetMHCcons and MHCflurry. Below are the details of the errors (taken from my .out log file, I've also copied my exact command below this):

==========================================
SLURM_JOB_ID = 27728089
SLURM_JOB_NODELIST = a01-15,b02-[15,20],b04-14,b09-[13-14],b17-[14,16],b18-16,d23-[14-16]
TMPDIR = /tmp/SLURM_27728089
==========================================
Executing MHC Class I predictions
Converting .vcf to TSV
TSV file already exists. Skipping.
Converting VCF to TSV
Warning: Proximal variant is not a missense mutation and will be skipped: chr1 152910385
Warning: Proximal variant is not a missense mutation and will be skipped: chr7 6005908
Warning: Proximal variant is not a missense mutation and will be skipped: chr7 6005908
Warning: Proximal variant is not a missense mutation and will be skipped: chr7 6005908
Warning: Proximal variant is not a missense mutation and will be skipped: chr7 6005905
Warning: Proximal variant is not a missense mutation and will be skipped: chr7 6005905
Warning: Proximal variant is not a missense mutation and will be skipped: chr7 6005905
Warning: Proximal variant is not a missense mutation and will be skipped: chr11 96092208
Warning: Proximal variant is not a missense mutation and will be skipped: chr11 96092208
Warning: Proximal variant is not a missense mutation and will be skipped: chr11 96092206
Warning: Proximal variant is not a missense mutation and will be skipped: chr11 96092206
Warning: Proximal variant is not a missense mutation and will be skipped: chr14 69573503
Warning: Proximal variant is not a missense mutation and will be skipped: chr14 69573497
Warning: Proximal variant is not a missense mutation and will be skipped: chrM 12705
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 1-100
Split TSV file for Entries 1-100 already exists. Skipping.
Splitting TSV into smaller chunks - Entries 101-200
Split TSV file for Entries 101-200 already exists. Skipping.
Splitting TSV into smaller chunks - Entries 201-300
Split TSV file for Entries 201-300 already exists. Skipping.
Splitting TSV into smaller chunks - Entries 301-391
Split TSV file for Entries 301-391 already exists. Skipping.
Completed
Generating Variant Peptide FASTA and Key Files
Split FASTA file for Epitope Length 8 - Entries 1-200 already exists. Skipping.
Split FASTA file for Epitope Length 9 - Entries 1-200 already exists. Skipping.
Split FASTA file for Epitope Length 10 - Entries 1-200 already exists. Skipping.
Split FASTA file for Epitope Length 11 - Entries 1-200 already exists. Skipping.
Split FASTA file for Epitope Length 8 - Entries 201-400 already exists. Skipping.
Split FASTA file for Epitope Length 9 - Entries 201-400 already exists. Skipping.
Split FASTA file for Epitope Length 10 - Entries 201-400 already exists. Skipping.
Split FASTA file for Epitope Length 11 - Entries 201-400 already exists. Skipping.
Split FASTA file for Epitope Length 8 - Entries 401-600 already exists. Skipping.
Split FASTA file for Epitope Length 9 - Entries 401-600 already exists. Skipping.
Split FASTA file for Epitope Length 10 - Entries 401-600 already exists. Skipping.
Split FASTA file for Epitope Length 11 - Entries 401-600 already exists. Skipping.
Split FASTA file for Epitope Length 8 - Entries 601-782 already exists. Skipping.
Split FASTA file for Epitope Length 9 - Entries 601-782 already exists. Skipping.
Split FASTA file for Epitope Length 10 - Entries 601-782 already exists. Skipping.
Split FASTA file for Epitope Length 11 - Entries 601-782 already exists. Skipping.
Completed
Epitope Length 8 is not valid for Method DeepImmuno and Allele HLA-A*02:01. Skipping.
Epitope Length 11 is not valid for Method DeepImmuno and Allele HLA-A*02:01. Skipping.
Allele HLA-A*32:01 not valid for Method DeepImmuno. Skipping.
Epitope Length 8 is not valid for Method SMM and Allele HLA-A*32:01. Skipping.
Epitope Length 8 is not valid for Method SMMPMBEC and Allele HLA-A*32:01. Skipping.
Epitope Length 11 is not valid for Method SMM and Allele HLA-A*32:01. Skipping.
Epitope Length 11 is not valid for Method SMMPMBEC and Allele HLA-A*32:01. Skipping.
Epitope Length 8 is not valid for Method DeepImmuno and Allele HLA-B*18:01. Skipping.
Epitope Length 11 is not valid for Method DeepImmuno and Allele HLA-B*18:01. Skipping.
Allele HLA-B*35:12 not valid for Method DeepImmuno. Skipping.
Allele HLA-B*35:12 not valid for Method NetMHC. Skipping.
Allele HLA-B*35:12 not valid for Method SMM. Skipping.
Allele HLA-B*35:12 not valid for Method SMMPMBEC. Skipping.
Epitope Length 8 is not valid for Method DeepImmuno and Allele HLA-C*04:01. Skipping.
Epitope Length 8 is not valid for Method SMM and Allele HLA-C*04:01. Skipping.
Epitope Length 8 is not valid for Method SMMPMBEC and Allele HLA-C*04:01. Skipping.
Epitope Length 10 is not valid for Method SMM and Allele HLA-C*04:01. Skipping.
Epitope Length 10 is not valid for Method SMMPMBEC and Allele HLA-C*04:01. Skipping.
Epitope Length 11 is not valid for Method DeepImmuno and Allele HLA-C*04:01. Skipping.
Epitope Length 11 is not valid for Method SMM and Allele HLA-C*04:01. Skipping.
Epitope Length 11 is not valid for Method SMMPMBEC and Allele HLA-C*04:01. Skipping.
Prediction file for Allele HLA-A*02:01 and Epitope Length 11 with Method NetMHCpanEL (Entries 201-400) already exists. Skipping.
Prediction file for Allele HLA-A*02:01 and Epitope Length 11 with Method PickPocket (Entries 201-400) already exists. Skipping.
Prediction file for Allele HLA-A*02:01 and Epitope Length 11 with Method SMM (Entries 201-400) already exists. Skipping.
Prediction file for Allele HLA-A*02:01 and Epitope Length 11 with Method SMMPMBEC (Entries 201-400) already exists. Skipping.
Prediction file for Allele HLA-A*32:01 and Epitope Length 11 with Method NetMHCpanEL (Entries 401-600) already exists. Skipping.
Prediction file for Allele HLA-A*32:01 and Epitope Length 11 with Method PickPocket (Entries 401-600) already exists. Skipping.
Prediction file for Allele HLA-A*02:01 and Epitope Length 11 with Method NetMHCpanEL (Entries 601-782) already exists. Skipping.
Prediction file for Allele HLA-A*02:01 and Epitope Length 11 with Method PickPocket (Entries 601-782) already exists. Skipping.
Prediction file for Allele HLA-A*02:01 and Epitope Length 11 with Method SMM (Entries 601-782) already exists. Skipping.
Prediction file for Allele HLA-A*02:01 and Epitope Length 11 with Method SMMPMBEC (Entries 601-782) already exists. Skipping.
Making binding predictions on Allele HLA-A*32:01 and Epitope Length 11 with Method NetMHC - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.ann.HLA-A*32:01.11.tsv_1-200
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 11 with Method NetMHC - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.ann.HLA-A*02:01.11.tsv_201-400
Making binding predictions on Allele HLA-B*18:01 and Epitope Length 11 with Method MHCnuggetsI - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.MHCnuggetsI.HLA-B*18:01.11.tsv_201-400
Making binding predictions on Allele HLA-B*35:12 and Epitope Length 11 with Method NetMHCpanEL - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.netmhcpan_el.HLA-B*35:12.11.tsv_1-200
Making binding predictions on Allele HLA-A*32:01 and Epitope Length 11 with Method NetMHCcons - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.netmhccons.HLA-A*32:01.11.tsv_401-600
Making binding predictions on Allele HLA-C*04:01 and Epitope Length 8 with Method BigMHC_EL - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_EL.HLA-C*04:01.8.tsv_401-600
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 8 with Method BigMHC_IM - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_IM.HLA-A*02:01.8.tsv_401-600
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 11 with Method NetMHCcons - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.netmhccons.HLA-A*02:01.11.tsv_601-782
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 8 with Method BigMHC_EL - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_EL.HLA-A*02:01.8.tsv_1-200
Making binding predictions on Allele HLA-B*18:01 and Epitope Length 11 with Method MHCnuggetsI - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.MHCnuggetsI.HLA-B*18:01.11.tsv_601-782
2024-11-22:08:36:13,647 ERROR    [netmhccons_1_1_python_interface.py:85] len(peptide_list) != len(scores) -- 10 != 0

Traceback (most recent call last):
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py", line 516, in <module>
    Prediction().main()
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py", line 507, in main
    self.commandline_input(args)
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py", line 132, in commandline_input
2024-11-22:08:36:13,649 ERROR    [netmhccons_1_1_python_interface.py:85] len(peptide_list) != len(scores) -- 10 != 0

Traceback (most recent call last):
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py", line 516, in <module>
    mhc_scores = mhc_predictor.predict(input.input_protein.as_amino_acid_text())
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/seqpredictor.py", line 903, in predict
    Prediction().main()
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py", line 507, in main
    self.commandline_input(args)
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py", line 132, in commandline_input
    mhc_scores = mhc_predictor.predict(input.input_protein.as_amino_acid_text())
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/seqpredictor.py", line 903, in predict
    scores.append(predictor.predict_sequence(sequence,pred))
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/seqpredictor.py", line 479, in predict_sequence
    scores.append(predictor.predict_sequence(sequence,pred))
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/seqpredictor.py", line 479, in predict_sequence
    scores = predict_netmhccons(sequence, (allele_name_or_sequence, self.length))
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 22, in predict_sequence
    scores = predict_netmhccons(sequence, (allele_name_or_sequence, self.length))
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 22, in predict_sequence
    scores += predict_peptide_list(peptide_list, allele_length_pair)
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 86, in predict_peptide_list
    scores += predict_peptide_list(peptide_list, allele_length_pair)
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 86, in predict_peptide_list
    raise Exception(msg)
Exception: len(peptide_list) != len(scores) -- 10 != 0
    raise Exception(msg)
Exception: len(peptide_list) != len(scores) -- 10 != 0
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 11 with Method NetMHC - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.ann.HLA-A*02:01.11.tsv_201-400 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 11 with Method NetMHCcons - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.netmhccons.HLA-A*02:01.11.tsv_201-400
2024-11-22:08:36:35,223 ERROR    [netmhccons_1_1_python_interface.py:85] len(peptide_list) != len(scores) -- 11 != 0

Traceback (most recent call last):
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py", line 516, in <module>
    Prediction().main()
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py", line 507, in main
    self.commandline_input(args)
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py", line 132, in commandline_input
    mhc_scores = mhc_predictor.predict(input.input_protein.as_amino_acid_text())
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/seqpredictor.py", line 903, in predict
    scores.append(predictor.predict_sequence(sequence,pred))
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/seqpredictor.py", line 479, in predict_sequence
    scores = predict_netmhccons(sequence, (allele_name_or_sequence, self.length))
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 22, in predict_sequence
    scores += predict_peptide_list(peptide_list, allele_length_pair)
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 86, in predict_peptide_list
    raise Exception(msg)
Exception: len(peptide_list) != len(scores) -- 11 != 0
Making binding predictions on Allele HLA-A*32:01 and Epitope Length 11 with Method NetMHC - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.ann.HLA-A*32:01.11.tsv_1-200 - Completed
Making binding predictions on Allele HLA-A*32:01 and Epitope Length 11 with Method NetMHCcons - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.netmhccons.HLA-A*32:01.11.tsv_1-200
2024-11-22:08:36:35,951 ERROR    [netmhccons_1_1_python_interface.py:85] len(peptide_list) != len(scores) -- 11 != 0

Traceback (most recent call last):
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py", line 516, in <module>
    Prediction().main()
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py", line 507, in main
    self.commandline_input(args)
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py", line 132, in commandline_input
    mhc_scores = mhc_predictor.predict(input.input_protein.as_amino_acid_text())
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/seqpredictor.py", line 903, in predict
    scores.append(predictor.predict_sequence(sequence,pred))
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/seqpredictor.py", line 479, in predict_sequence
    scores = predict_netmhccons(sequence, (allele_name_or_sequence, self.length))
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 22, in predict_sequence
    scores += predict_peptide_list(peptide_list, allele_length_pair)
  File "/scratch1/seetaraj/pvacseq_bin/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 86, in predict_peptide_list
    raise Exception(msg)
Exception: len(peptide_list) != len(scores) -- 11 != 0
Making binding predictions on Allele HLA-B*35:12 and Epitope Length 11 with Method NetMHCpanEL - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.netmhcpan_el.HLA-B*35:12.11.tsv_1-200 - Completed
Making binding predictions on Allele HLA-B*35:12 and Epitope Length 11 with Method PickPocket - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.pickpocket.HLA-B*35:12.11.tsv_1-200
Making binding predictions on Allele HLA-B*35:12 and Epitope Length 11 with Method PickPocket - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.pickpocket.HLA-B*35:12.11.tsv_1-200 - Completed
Making binding predictions on Allele HLA-C*04:01 and Epitope Length 8 with Method BigMHC_EL - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_EL.HLA-C*04:01.8.tsv_1-200
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 8 with Method BigMHC_EL - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_EL.HLA-A*02:01.8.tsv_1-200 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 8 with Method BigMHC_IM - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_IM.HLA-A*02:01.8.tsv_1-200
Making binding predictions on Allele HLA-C*04:01 and Epitope Length 8 with Method BigMHC_EL - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_EL.HLA-C*04:01.8.tsv_1-200 - Completed
Making binding predictions on Allele HLA-C*04:01 and Epitope Length 8 with Method BigMHC_IM - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_IM.HLA-C*04:01.8.tsv_1-200
Making binding predictions on Allele HLA-C*04:01 and Epitope Length 8 with Method BigMHC_EL - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_EL.HLA-C*04:01.8.tsv_401-600 - Completed
Making binding predictions on Allele HLA-C*04:01 and Epitope Length 8 with Method BigMHC_IM - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_IM.HLA-C*04:01.8.tsv_401-600
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 8 with Method BigMHC_IM - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_IM.HLA-A*02:01.8.tsv_401-600 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 8 with Method MHCflurry - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.MHCflurry.HLA-A*02:01.8.tsv_401-600
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 8 with Method BigMHC_IM - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_IM.HLA-A*02:01.8.tsv_1-200 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 8 with Method MHCflurry - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.MHCflurry.HLA-A*02:01.8.tsv_1-200
Making binding predictions on Allele HLA-C*04:01 and Epitope Length 8 with Method BigMHC_IM - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_IM.HLA-C*04:01.8.tsv_401-600 - Completed
Making binding predictions on Allele HLA-C*04:01 and Epitope Length 8 with Method MHCflurry - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.MHCflurry.HLA-C*04:01.8.tsv_401-600
Making binding predictions on Allele HLA-C*04:01 and Epitope Length 8 with Method BigMHC_IM - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.BigMHC_IM.HLA-C*04:01.8.tsv_1-200 - Completed
Making binding predictions on Allele HLA-C*04:01 and Epitope Length 8 with Method MHCflurry - File /scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.MHCflurry.HLA-C*04:01.8.tsv_1-200
An exception occured in thread 8: (<class 'subprocess.CalledProcessError'>, Command '['/scratch1/seetaraj/.conda/envs/biomodal/bin/python', '/scratch1/seetaraj/pvacseq_bin/mhc_i/src/predict_binding.py', 'netmhccons', 'HLA-A*02:01', '11', '/scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.11.fa.split_601-782']' returned non-zero exit status 1.).
Traceback (most recent call last):
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/pvactools/lib/prediction_class.py", line 513, in predict
    response = run(arguments, check=True, stdout=DEVNULL, stderr=stderr_fh)
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/subprocess.py", line 526, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['mhcflurry-predict', '--alleles', 'HLA-A*02:01', '--out', '/scratch1/seetaraj/moonshot_neoantigen/somatic_vcfs/pvacseq_input_prep/RUN_FOLDER_PVACSEQ/C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L/MHC_Class_I/tmp/tmpsxlc7dk6', '--peptides', 'RVRWEDVE', 'TKGRTFEE', 'ARGQRPRV', 'PLTVDEIA', 'IRRYTEIS', 'QSRPCPYS', 'TQLARECG', 'ITTYKCEC', 'PDPTGKFN', 'GKSIIQTP', 'NQLEKWMK', 'PSSFFSAA', 'SAVLSTPL', 'PMSCPYYL', 'EKWYIPDP', 'LVLMFLGH', 'CRQTNNQQ', 'GGALVLVF', 'CPLQYSTE', 'KVPLTVEE', 'YSRTLAGS', 'AAVPAAAG', 'LNVEEGLY', 'AGNSSQSH', 'PLPPAPPT', 'LELPEQQE', 'FTLDPPGS', 'ERIRKLSM', 'RTFEEIAS', 'DSKRRQTN', 'ELSEQQEG', 'GRWEDVEP', 'RETTVIWD', 'EKWMKLNV', 'QGVPGAPG', 'QNITNQLE', 'RRQTNNQQ', 'WRVRWEDV', 'IRIAREAP', 'SGSKKMFS', 'GGAAAAQG', 'HFTLDPSG', 'AAAARGQR', 'VLVFLGFQ', 'TYKCECVA', 'LVPGVGGA', 'ASGKSIQT', 'MDTASSTA', 'KFNLIRRY', 'VRHLGSSA', 'EEYTQLAR', 'PEKAVPNV', 'NVRHLGSS', 'GSITTPPL', 'KGVPGAPG', 'QYYLLSDG', 'LIRRYTEI', 'SVMLMCFV', 'TEARTCSC', 'LLLCLFCM', 'RKAVATCS', 'GDSCPLQY', 'TLDPSGSK', 'FFLCVCVS', 'DFFVCVCL', 'KLLHWNGH', 'QPDSKRRQ', 'VSNQRATT', 'VASGKSII', 'DVIVQGDI', 'VCYAGYRL', 'DPSGSKKM', 'NQYNYIGY', 'PFVPPSSF', 'NQICLPNR', 'FVCVCLSS', 'ETVPPLNE', 'VEEIASFG', 'NVEEGLYS', 'NPGGYECG', 'PDSKRRQT', 'AVAMVSVL', 'YECGCYAG', 'SHFTLDPP', 'KQQLCGFW', 'SIIQTPQS', 'QQLCGFRR', 'AARAVAVV', 'RPLPPAPP', 'EEIASFGE', 'NLTEWKRQ', 'GYLDYKKE', 'LLCLFCMP', 'AARAVAMV', 'TKGRTFDE', 'LSTPLWEW', 'RRAAGSGF', 'ETVKNPDE', 'KVPLTVDE', 'KAAKLLHW', 'GVFVANLT', 'LQYSTEAR', 'ASELWRGR', 'VGGALVLM', 'KYYKISVV', 'VSNQRETT', 'FEEIASGF', 'YIGYLDYK', 'ELQGAISW', 'PEQQEGQL', 'AVPAAAGS', 'KLSMKAST', 'AGSITTPP', 'KRYSPQFV', 'DLMLCLFC', 'VLMFLGFQ', 'ASELWRVR', 'AEGRKKAF', 'DFFLCVCV', 'QRATTVIW', 'KISVVLMC', 'WNGHLKPW', 'LEKWMKLN', 'SMKPVIFL', 'QGDSCPLQ', 'CVCYAGYR', 'GGYECVCY', 'KRRQTNNQ', 'DLLLCLFC', 'MLCLFCMP', 'AGNQYNYI', 'SAVLSTLL', 'PDSKCRQT', 'EKAVPNMA', 'VMLMCFVV', 'SWEAPVEK', 'WNVRHLGS', 'ETGKNPDE', 'ELQGAIPW', 'DSKCRQTN', 'KIRIAREA', 'FITTYKCE', 'TFEGETGK', 'QQLCGFWR', 'VVSVLVVV', 'PVIFLPFT', 'LVLVFLGF', 'VIVQGDIL', 'RTCSCIFR', 'VWEKWYIP', 'VSDLMLCL', 'VIVQGDSC', 'TEWKRQNI', 'RARAARRA', 'AAVPAAAV', 'TVDEIASF', 'PPLKELTE', 'IKVPLTVE', 'TIDPMWNV', 'VPPSSFFS', 'HTMDTASS', 'SCQYYLLS', 'YVASGKSI', 'NSSQSHPC', 'YNQPDSKC', 'RHLGSSAG', 'SAGKRYSP', 'AAAVPRAR', 'NSAEGRKR', 'ITTCKCEC', 'GYECVCYA', 'DEIASFGE', 'EARTCSCI', 'DPTGKFNL', 'GALVLMFL', 'PNMANLVE', 'GKRYSPQF', 'KGRTFEEI', 'GALVLVFL', 'VVLMCFVV', 'TQGVPGAP', 'HLKPWGRT', 'GRTFDEIA', 'KKERIRKL', 'FVANLTEW', 'AVAVVSVL', 'PGGYECGC', 'QICLPNRQ', 'EYTQLARE', 'MANLVEAD', 'ITREAPSE', 'KPVILALY', 'SSQSRPCP', 'RAAGSGFR', 'QEGQLELS', 'LPNRQHVV', 'MAKIRIAR', 'EGQLELSE', 'AVVSVLVV', 'VIRGAGNQ', 'LWRVRWED', 'KPNFITTC', 'VRWEDVEP', 'PQFVKAAK', 'FNPGVFVA', 'VPNVANLV', 'PRARAARR', 'GAGNQYNY', 'YTEISNIK', 'GAAAVPAA', 'DVIVQGDS', 'QHSTIDPM', 'PGHAAAFS', 'EGRKKAFA', 'ASYTDVWE', 'SSQSHPCP', 'STLLWEWV', 'LAVSDLLL', 'AVPAAAVP', 'EPGLQGTK', 'ELWRVRWE', 'VQGDSCPL', 'NMANLVEA', 'GQLELPEQ', 'MKLNVEEG', 'NELTEVPG', 'AARRAAGS', 'KLNVEEGL', 'TFDEIASG', 'ESMKPVIL', 'AAAAQGQR', 'CLPNRQHV', 'RIAREAPS', 'NFITTYKC', 'GLQGTKGV', 'RKLSMKAS', 'IPMSCPYY', 'LMLCLFCM', 'WYIPDPTG', 'SAARAVAM', 'MKPVILAL', 'AARGQRPR', 'SMKASTCS', 'NSSQSRPC', 'LKPGHAAA', 'CLPNHQHV', 'FITTCKCE', 'SEAEGRRK', 'GDILALYN', 'TCSFNPGV', 'ETKGRTFD', 'NFITTCKC', 'PLQYSTEA', 'SITTPPLL', 'EGRKRPLP', 'DILALYNT', 'PMSCQYYL', 'TTPPLLIV', 'KSIIQTPQ', 'GVSNQRAT', 'KERIRKLS', 'KRQNITNQ', 'TDTASSTA', 'AVPRARAA', 'PGGYECVC', 'LQGAISWE', 'SPQFVKAA', 'LTRECGLW', 'STEARTCS', 'ASGKSIIQ', 'TKGVPGAP', 'EGETGKNP', 'PNRQHVVY', 'YNQPDSKR', 'EGRRKAVA', 'KGRTFDEI', 'ALYNTALK', 'LAGSITTP', 'ECVCYAGY', 'FNLIRRYT', 'MLMCFVVP', 'HLGSSAGK', 'PEKAVPNM', 'HMAKIRIA', 'SHFTLDPS', 'IRKLSMKA', 'VAMVSVLV', 'GAAAAQGQ', 'CPYYLLSD', 'NRQHVVYG', 'KVVIRGAG', 'WRGRWEDV', 'PPLNELTE', 'RKRPLPPA', 'YDFFLCVC', 'ARAVAMVS', 'PHFLGPGV', 'NITNQLEK', 'SSFYDFFV', 'TMDTASST', 'VSDLLLCL', 'KPWGRTAS', 'MFLGHCAA', 'EYTQLTRE', 'GQLELSEQ', 'KYYKISVM', 'SELWRGRW', 'TQLTRECG', 'KWMKLNVE', 'GSAHTMDT', 'FYDFFVCV', 'SSAGKRYS', 'SAHTTDTA', 'SAEGRKRP', 'NYIGYLDY', 'GGGSAHTM', 'NQICLPNH', 'VSAVLSTL', 'WKRQNITN', 'SYTDVWEK', 'GGALVLMF', 'ATTVIWDK', 'PPLLIVFY', 'VLMCFVVP', 'QGAISWEA', 'EGLYSRTL', 'PTGKFNLI', 'HFLGPGVG', 'SCPLQYST', 'SPHFLVPG', 'LETVPPLN', 'LELQGAIP', 'ETTVIWDK', 'QICLPNHQ', 'GSAHTTDT', 'SAHTMDTA', 'VIFLPFTI', 'YECVCYAG', 'VPPLNELT', 'VAVVSVLV', 'DSASTKVV', 'SIQTPQSH', 'SRFFSAAA', 'TTDTASST', 'GGAAAARG', 'NQPDSKCR', 'ALVLVFLG', 'FRRGSEER', 'TVPPLNEL', 'PFVPPSRF', 'MSEAEGRG', 'SKCRQTNN', 'SAEGRKKA', 'AISWEAPV', 'TVEEIASF', 'ESMKPVIF', 'LARECGLW', 'LDPSGSKK', 'AAAQGQRP', 'VFYQQHST', 'MSCPYYLL', 'TVPPLKEL', 'SFYDFFVC', 'LMFLGHCA', 'IRITREAP', 'AVSDLMLC', 'FYDFFLCV', 'DCDSASTK', 'SCPYYLLS', 'YNTALKPG', 'MSEAEGRR', 'QGTQGVPG', 'RPCPYSEI', 'TREAPSEC', 'QRETTVIW', 'YTDVWEKW', 'KPNFITTY', 'CSFNPGVF', 'ETVPPLKE', 'GNSSQSRP', 'WEKWYIPD', 'PWEAPVEK', 'PNFITTYK', 'GGSAHTMD', 'GIPMSCPY', 'FVPPSRFF', 'IDPMWNVR', 'CDSASTKV', 'HPCPYSEI', 'FLCVCVSP', 'PPSSFFSA', 'KIRITREA', 'EDCDSAST', 'AKIRITRE', 'LNELTEVP', 'ILALYNTA', 'VANLVEAD', 'FTFEGETG', 'TCKCECVA', 'EEYTQLTR', 'EGIPMSCP', 'YKISVVLM', 'LVFLGHCA', 'NTALKPGH', 'IPWEAPVE', 'GRTASYTD', 'GRKRPLPP', 'SFNPGVFV', 'QFVKAAKL', 'VLSTLLWE', 'LVLVFLGH', 'SKRRQTNN', 'AAAFSEDC', 'LTEWKRQN', 'NLIRRYTE', 'YKISVMLM', 'LASELWRV', 'ALVLMFLG', 'LCGFRRGS', 'RTLAGSIT', 'PLWEWVLQ', 'LLHWNGHL', 'GHAAAFSE', 'FTFEGETV', 'TTCKCECV', 'IPMSCQYY', 'ECGCYAGY', 'YIPDPTGK', 'GCYAGYRL', 'NQRETTVI', 'LSTLLWEW', 'SRPCPYSE', 'TFEGETVK', 'CGCYAGYR', 'PNFITTCK', 'LSEQQEGQ', 'PYYLLSDG', 'VGGALVLV', 'FTLDPSGS', 'QPDSKCRQ', 'AEGRRKAV', 'RAARRAAG', 'LEEYTQLT', 'VPAAAVPR', 'GNQYNYIG', 'SPHFLGPG', 'IVFYQQHS', 'QLELPEQQ', 'RIRKLSMK', 'RITREAPS', 'SQSRPCPY', 'DPPGSKKM', 'SFSPHFLG', 'TALKPGHA', 'LSMKASTC', 'VKNPDEED', 'PLNELTEV', 'VKAAKLLH', 'QQHSTIDP', 'LKPWGRTA', 'ARAARRAA', 'PGLQGTQG', 'LVFLGFQD', 'STCSFNPG', 'RQNITNQL', 'QLCGFRRG', 'NPGGYECV', 'IKVPLTVD', 'PNVANLVE', 'SNQRATTV', 'GPGVGGAA', 'KWYIPDPT', 'LAVSDLML', 'FVKAAKLL', 'AGAAAVPA', 'VILALYNT', 'PLLIVFYQ', 'AAFSEDCD', 'QLARECGL', 'CGFRRGSE', 'SGKSIIQT', 'PHFLVPGV', 'AFSEDCDS', 'DVWEKWYI', 'IPDPTGKF', 'EKAVPNVA', 'KISVMLMC', 'YNYIGYLD', 'VVIRGAGN', 'FPFVPPSR', 'SEQQEGQL', 'ITTPPLLI', 'AKLLHWNG', 'ISWEAPVE', 'YYKISVVL', 'EGGAAAAQ', 'QGQRPRVP', 'AVLSTPLW', 'PMWNVRHL', 'TPPLLIVF', 'SDLMLCLF', 'PSRFFSAA', 'AEGRGKAV', 'MKPVIFLP', 'STIDPMWN', 'DEIASGFR', 'YTQLAREC', 'AGKRYSPQ', 'PWGRTASY', 'GKSIQTPQ', 'LLWEWVLQ', 'LTVEEIAS', 'LETVPPLK', 'LIVFYQQH', 'MAKIRITR', 'LALYNTAL', 'RGAGNQYN', 'FLGPGVGG', 'SFYDFFLC', 'TLDPPGSK', 'PAAAVPRA', 'EGRGKAVA', 'EPGLQGTQ', 'DSCPLQYS', 'FFVCVCLS', 'QGTKGVPG', 'AVPNVANL', 'GKAVATCS', 'VSAVLSTP', 'GRGKAVAT', 'VDEIASFG', 'GETGKNPD', 'HSTIDPMW', 'SRTLAGSI', 'LQGAIPWE', 'LQGTKGVP', 'RAVAVVSV', 'SLAVSDLL', 'AVSDLLLC', 'RGQRPRVP', 'YSPQFVKA', 'TPLWEWVL', 'GHLKPWGR', 'EGQLELPE', 'QLEKWMKL', 'LPEQQEGQ', 'MKASTCSF', 'GYECGCYA', 'GTQGVPGA', 'YLDYKKER', 'LHWNGHLK', 'AMVSVLVV', 'GFRRGSEE', 'KELTEVPG', 'CVCLSSNR', 'AGNSSQSR', 'ARAVAVVS', 'AAKLLHWN', 'GAIPWEAP', 'SFSPHFLV', 'GRTFEEIA', 'TASYTDVW', 'STPLWEWV', 'EGGAAAAR', 'LGPGVGGA', 'EWKRQNIT', 'RRKAVATC', 'LYNTALKP', 'SDLLLCLF', 'PNHQHVVY', 'EEIASGFR', 'VASGKSIQ', 'QLCGFWRG', 'WRGSEERT', 'SASTKVVI', 'VPPLKELT', 'CGFWRGSE', 'LDYKKERI', 'NPGVFVAN', 'VEEGLYSR', 'LYSRTLAG', 'RQHVVYGP', 'VPLTVEEI', 'KRPLPPAP', 'LVLMFLGF', 'AQGQRPRV', 'DPMWNVRH', 'GRKKAFAT', 'VFVANLTE', 'TRECGLWL', 'SEAEGRGK', 'RYTEISNI', 'ELPEQQEG', 'QEGQLELP', 'IVQGDILA', 'GETVKNPD', 'QSHPCPYS', 'PGVFVANL', 'LLIVFYQQ', 'VLVFLGHC', 'RRGSEERT', 'VPLTVDEI', 'IAREAPSE', 'LMFLGFQD', 'SMKPVILA', 'FLVPGVGG', 'FEGETVKN', 'GNSSQSHP', 'GGGSAHTT', 'LASELWRG', 'NHQHVVYG', 'ETKGRTFE', 'RGKAVATC', 'LDPPGSKK', 'GLYSRTLA', 'FYQQHSTI', 'ASTCSFNP', 'YKKERIRK', 'VPNMANLV', 'MSCQYYLL', 'HFTLDPPG', 'PGLQGTKG', 'NGHLKPWG', 'FSEDCDSA', 'AAQGQRPR', 'VLMFLGHC', 'LTVDEIAS', 'GAISWEAP', 'STKVVIRG', 'KPVIFLPF', 'TGKFNLIR', 'AEGRKRPL', 'FDEIASGF', 'IRGAGNQY', 'LELQGAIS', 'AHTMDTAS', 'VQGDILAL', 'WMKLNVEE', 'SQSHPCPY', 'PPSRFFSA', 'HAAAFSED', 'HFLVPGVG', 'AVLSTLLW', 'TGKNPDEE', 'ALKPGHAA', 'FWRGSEER', 'YTQLTREC', 'EAEGRRKA', 'FSPHFLGP', 'RRYTEISN', 'LPNHQHVV', 'FEGETGKN', 'MNSAEGRK', 'ITNQLEKW', 'GVSNQRET', 'NQRATTVI', 'DYVASGKS', 'TLLWEWVL', 'PAAAGSGF', 'PSGSKKMF', 'RKKAFATC', 'AAVPRARA', 'HWNGHLKP', 'EGIPMSCQ', 'SELWRVRW', 'RAVAMVSV', 'AAARGQRP', 'VCVCLSSN', 'ARECGLWL', 'AVPNMANL', 'SVVLMCFV', 'VPRARAAR', 'ARRAAGSG', 'NVANLVEA', 'KASTCSFN', 'PPGSKKMF', 'TLAGSITT', 'CQYYLLSD', 'HTTDTASS', 'IGYLDYKK', 'TVKNPDEE', 'SLAVSDLM', 'YSTEARTC', 'GIPMSCQY', 'MFLGFQDV', 'QLTRECGL', 'EAEGRGKA', 'RATTVIWD', 'SSFFSAAA', 'KAVPNMAN', 'FVPPSSFF', 'GLQGTQGV', 'TKVVIRGA', 'EGETVKNP', 'GFWRGSEE', 'LGSSAGKR', 'GKFNLIRR', 'NSAEGRKK', 'SGKSIQTP', 'ISVMLMCF', 'VFLGFQDV', 'CSCIFRRL', 'VLSTPLWE', 'GESMKPVI', 'GTKGVPGA', 'TFEEIASG', 'SEDCDSAS', 'VGVSNQRE', 'RGRWEDVE', 'VPGVGGAA', 'RTFDEIAS', 'EEGLYSRT', 'KPGHAAAF', 'SNQRETTV', 'CKCECVAP', 'GRRKAVAT', 'AKIRIARE', 'VPAAAGSG', 'MVSVLVVV', 'RFFSAAAA', 'LWRGRWED', 'LKELTEVP', 'GGYECGCY', 'AREAPSEC', 'HMAKIRIT', 'DYKKERIR', 'RYSPQFVK', 'IIQTPQSH', 'QGAIPWEA', 'AAAGSGFR', 'TDVWEKWY', 'LEEYTQLA', 'ICLPNRQH', 'HQHVVYGP', 'SAARAVAV', 'GSSAGKRY', 'NQPDSKRR', 'KCRQTNNQ', 'TCSCIFRR', 'GGSAHTTD', 'ASTKVVIR', 'YDFFVCVC', 'PLTVEEIA', 'PLKELTEV', 'SSFYDFFL', 'KQQLCGFR', 'TTYKCECV', 'PGSKKMFS', 'KAVPNVAN', 'AIPWEAPV', 'PVILALYN', 'QYSTEART', 'ARTCSCIF', 'YQQHSTID', 'LCGFWRGS', 'SHPCPYSE', 'GAAAARGQ', 'VCLSSNRL', 'VFLGHCAA', 'SFFSAAAA', 'ICLPNHQH', 'VANLTEWK', 'QLELSEQQ', 'GKNPDEED', 'ELWRGRWE', 'VGVSNQRA', 'FPFVPPSS', 'ISVVLMCF', 'TNQLEKWM', 'MWNVRHLG', 'VPPSRFFS', 'YYKISVML', 'ANLTEWKR', 'YKCECVAP', 'AAAVPAAA', 'WGRTASYT', 'AHTTDTAS', 'QYNYIGYL', 'IVQGDSCP', 'LELSEQQE', 'RTASYTDV', 'LQGTQGVP', 'FSPHFLVP', 'KSIQTPQS', 'QGDILALY']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/pvactools/lib/pipeline.py", line 357, in call_iedb
    pvactools.lib.call_iedb.main(arguments)
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/pvactools/lib/call_iedb.py", line 46, in main
    raise err
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/pvactools/lib/call_iedb.py", line 41, in main
    (response_text, output_mode) = prediction_class_object.predict(args.input_file, args.allele, args.epitope_length, args.iedb_executable_path, args.iedb_retries, tmp_dir=args.tmp_dir, log_dir=args.log_dir)
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/pvactools/lib/prediction_class.py", line 519, in predict
    raise Exception("An error occurred while calling MHCflurry:\n{}".format(err))
Exception: An error occurred while calling MHCflurry:
2024-11-22 08:41:23.474385: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:485] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
2024-11-22 08:41:23.523558: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:8454] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
2024-11-22 08:41:23.536995: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1452] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2024-11-22 08:41:23.630362: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-11-22 08:41:25.202764: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-11-22 08:41:26.509223: E external/local_xla/xla/stream_executor/cuda/cuda_driver.cc:266] failed call to cuInit: CUDA_ERROR_UNKNOWN: unknown error
2024-11-22 08:41:26.509268: I external/local_xla/xla/stream_executor/cuda/cuda_diagnostics.cc:135] retrieving CUDA diagnostic information for host: a01-15.hpc.usc.edu
2024-11-22 08:41:26.509276: I external/local_xla/xla/stream_executor/cuda/cuda_diagnostics.cc:142] hostname: a01-15.hpc.usc.edu
2024-11-22 08:41:26.509332: I external/local_xla/xla/stream_executor/cuda/cuda_diagnostics.cc:166] libcuda reported version is: 535.129.3
2024-11-22 08:41:26.509362: I external/local_xla/xla/stream_executor/cuda/cuda_diagnostics.cc:170] kernel reported version is: 535.129.3
2024-11-22 08:41:26.509367: I external/local_xla/xla/stream_executor/cuda/cuda_diagnostics.cc:249] kernel version seems to match DSO: 535.129.3
Traceback (most recent call last):
  File "/scratch1/seetaraj/.conda/envs/biomodal/bin/mhcflurry-predict", line 8, in <module>
    sys.exit(run())
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/mhcflurry/predict_command.py", line 204, in run
    predictor = Class1PresentationPredictor.load(models_dir)
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/mhcflurry/class1_presentation_predictor.py", line 956, in load
    affinity_predictor = Class1AffinityPredictor.load(
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/mhcflurry/class1_affinity_predictor.py", line 608, in load
    optimized = result.optimize()
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/mhcflurry/class1_affinity_predictor.py", line 653, in optimize
    Class1NeuralNetwork.merge(
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/mhcflurry/class1_neural_network.py", line 1148, in merge
    configure_tensorflow()
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/mhcflurry/common.py", line 131, in configure_tensorflow
    tensorflow.compat.v1.keras.backend.set_session(session)
AttributeError: module 'keras._tf_keras.keras.backend' has no attribute 'set_session'. Did you mean: 'set_epsilon'?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/scratch1/seetaraj/.conda/envs/biomodal/bin/pvacseq", line 8, in <module>
    sys.exit(main())
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/pvactools/tools/pvacseq/main.py", line 130, in main
    args[0].func.main(args[1])
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/pvactools/tools/pvacseq/run.py", line 142, in main
    pipeline.execute()
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/pvactools/lib/pipeline.py", line 451, in execute
    self.call_iedb(chunks)
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/pvactools/lib/pipeline.py", line 349, in call_iedb
    with pymp.Parallel(self.n_threads) as p:
  File "/scratch1/seetaraj/.conda/envs/biomodal/lib/python3.10/site-packages/pymp/__init__.py", line 148, in __exit__
    raise exc_t(exc_val)
TypeError: CalledProcessError.__init__() missing 1 required positional argument: 'cmd'

SLURM script (just one sample was run as an example):

#!/bin/bash
#SBATCH -J pvactoolsTest
#SBATCH -o %x\_%j.out
#SBATCH -n 12
#SBATCH -N 12
#SBATCH -c 16
#SBATCH --mem=200G
#SBATCH -t 48:00:00
#SBATCH --account=salhia_618
#SBATCH --partition=gpu

export MKL_SERVICE_FORCE_INTEL=1
export MKL_THREADING_LAYER=GNU
export OMP_NUM_THREADS=4

module load nvhpc

VCF="C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L_indel.gx.vcf.gz" \
SAMPLE="C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L" \
PHASED_VCF="C030_004507_01_WF00018417_FAM0001_T1_KHS6C_D04586001D02L.vep.vcf.gz" \
NORMAL="C030_004507_01_WF00018417_FAM0001_C1_KHS6C_d04668901D02L" \
ALLELE="HLA-A*32:01,HLA-B*35:12,HLA-A*02:01,HLA-B*18:01,HLA-C*04:01" \
IEDB="/scratch1/seetaraj/pvacseq_bin/"

pvacseq run \
  ${VCF} \
  ${SAMPLE} \
  ${ALLELE} \
  all \
  ${SAMPLE}/ \
  -b 500 \
  --iedb-install-directory ${IEDB} \
  -t 10 \
  --normal-sample-name ${NORMAL} \
  --tdna-cov 10 \
  --trna-cov 10 \
  --tdna-vaf 0.25 \
  --trna-vaf 0.25 \
  -p ${PHASED_VCF}

Please let me know if I can provide additional information to help get this resolved. Any advice is appreciated. Thank you so much!

susannasiebert commented 4 days ago

This error usually indicates that the pVACseq run ran out of memory. How much memory is available to you? I would try reducing the number of threads and/or upping the amount of memory available. We usually run with 8 threads and 32Gb of memory. Does the OMP_NUM_THREADS env variable have any effect on the actual number of threads available? If so, you'll want to up that as well.