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openvax / vaxrank

Ranked vaccine peptides for personalized cancer immunotherapy
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Vaxrank fails at saving results when there are no vaccines available #114

Closed armish closed 6 years ago

armish commented 7 years ago

Since 4.0.0, a majority of my vaxrank runs within epidisco fail with the following error and I am assuming that is because for these failed run, there is no potential vaccine available:

2017-02-14 18:01:11,173 - vaxrank.cli:287 - INFO - Namespace(bam='/path/work/_v01_with-rna_Sample_-b37/48c604cad7ad8816b58d4a92dc5fc521_path_work__v01_with-rna_Sample_-b37_9705c51188d8c1f95ef367a49e232df8_filtered_bamsamtoolsmerge.bam', cosmic_vcf_filename='', drop_secondary_alignments=False, genome=None, include_mismatches_after_variant=False, json_variants=[], maf=[], max_mutations_in_report=40, max_reference_transcript_mismatches=2, max_vaccine_peptides_per_mutation=3, mhc_alleles='', mhc_alleles_file='/path/work/_v01_with-rna_Sample_-b37/b84b8054b069332c2785ba004659c7ac8f71489687b19440ddcac1ce16a303f2rna0-_T_C2D8edsl-concatseq2hla-workdirhlarp.csv', mhc_epitope_lengths=[8, 9, 10, 11], mhc_predictor='netmhccons', min_alt_rna_reads=3, min_epitope_score=0.001, min_mapping_quality=1, min_transcript_prefix_length=10, min_variant_sequence_coverage=1, output_ascii_report='/path/work/_v01_with-rna_Sample_-b37/0d771abdf8f60720cf3495c56a50c73aepidisco-40pepnetmhcconsb84b8054b069332c2785ba004659c7ac8f71489687b19440ddcac1ce16a303f2rna0-_T_C2D8edsl-concatseq2hla-workdirhlarppassed_somatic_combinedvaxrank/vaxrank-result.txt', output_csv='', output_final_review='', output_html_report='', output_json_file='', output_patient_id='UNKNOWN', output_pdf_report='/path/work/_v01_with-rna_Sample_-b37/0d771abdf8f60720cf3495c56a50c73aepidisco-40pepnetmhcconsb84b8054b069332c2785ba004659c7ac8f71489687b19440ddcac1ce16a303f2rna0-_T_C2D8edsl-concatseq2hla-workdirhlarppassed_somatic_combinedvaxrank/vaxrank-result.pdf', output_reviewed_by='', output_xlsx_report='/path/work/_v01_with-rna_Sample_-b37/0d771abdf8f60720cf3495c56a50c73aepidisco-40pepnetmhcconsb84b8054b069332c2785ba004659c7ac8f71489687b19440ddcac1ce16a303f2rna0-_T_C2D8edsl-concatseq2hla-workdirhlarppassed_somatic_combinedvaxrank/vaxrank-result.xlsx', padding_around_mutation=5, protein_sequence_length=20, use_duplicate_reads=False, vaccine_peptide_length=25, variant=[], variant_sequence_assembly=True, vcf=['/path/work/_v01_with-rna_Sample_-b37/6242eec0c3a2a65ba5ab136b38e3dcbe804f3995f0270bb58d58577fdc9cd8c3gatk_bqsred41b2cb5d309f5703c5aab75655d93agatk_bqsr_strelka-exome-defaultstrelka_output/results/passed_somatic_combined.vcf', '/path/work/_v01_with-rna_Sample_-b37/26160f7c5db17503fb83ea3d95da605c804f3995f0270bb58d58577fdc9cd8c3gatk_bqsred41b2cb5d309f5703c5aab75655d93agatk_bqsr_mutect-default-merged.vcf'])
2017-02-14 18:01:11,173 - vaxrank.cli:190 - WARNING - Please specify --output-patient-id if possible; defaulting to unknown
2017-02-14 18:01:11,186 - vaxrank.cli:214 - INFO - MHC alleles: ['HLA-A*03:01', 'HLA-A*68:01', 'HLA-B*07:02', 'HLA-B*44:02', 'HLA-C*07:04', 'HLA-C*07:04', 'HLA-DQA1*01:03', 'HLA-DQA1*05:01', 'HLA-DQB1*03:01', 'HLA-DQB1*06:03', 'HLA-DRB1*11:01', 'HLA-DRB1*13:01']
2017-02-14 18:01:11,214 - vaxrank.cli:216 - INFO - Variants: <VariantCollection from '/path/work/_v01_with-rna_Sample_-b37/26160f7c5db17503fb83ea3d95da605c804f3995f0270bb58d58577fdc9cd8c3gatk_bqsred41b2cb5d309f5703c5aab75655d93agatk_bqsr_mutect-default-merged.vcf,/path/work/_v01_with-rna_Sample_-b37/6242eec0c3a2a65ba5ab136b38e3dcbe804f3995f0270bb58d58577fdc9cd8c3gatk_bqsred41b2cb5d309f5703c5aab75655d93agatk_bqsr_strelka-exome-defaultstrelka_output/results/passed_somatic_combined.vcf' with 3 elements>
  -- Variant(contig='17', start=1933381, ref='G', alt='A', reference_name='GRCh37')
  -- Variant(contig='17', start=62502295, ref='C', alt='A', reference_name='GRCh37')
  -- Variant(contig='17', start=62502324, ref='C', alt='A', reference_name='GRCh37')
2017-02-14 18:01:11,256 - mhctools.cli.args:138 - INFO - Building MHC binding prediction type for alleles ['HLA-A*03:01', 'HLA-A*68:01', 'HLA-B*07:02', 'HLA-B*44:02', 'HLA-C*07:04', 'HLA-C*07:04', 'HLA-DQA1*01:03', 'HLA-DQA1*05:01', 'HLA-DQB1*03:01', 'HLA-DQB1*06:03', 'HLA-DRB1*11:01', 'HLA-DRB1*13:01'] and epitope lengths [8, 9, 10, 11]
2017-02-14 18:01:11,406 - mhctools.process_helpers:77 - INFO - netMHCcons took 0.1492 seconds
2017-02-14 18:01:11,407 - isovar.allele_reads:200 - INFO - Gathering reads for Variant(contig='17', start=1933381, ref='G', alt='A', reference_name='GRCh37')
2017-02-14 18:01:11,423 - isovar.allele_reads:208 - INFO - Gathering variant reads for variant Variant(contig='17', start=1933381, ref='G', alt='A', reference_name='GRCh37') (chromosome = 17, gene names = [])
2017-02-14 18:01:11,430 - isovar.locus_reads:302 - INFO - Found 0 reads overlapping locus 17: 1933380-1933382
2017-02-14 18:01:11,430 - isovar.translation:453 - INFO - No supporting reads for variant Variant(contig='17', start=1933381, ref='G', alt='A', reference_name='GRCh37')
2017-02-14 18:01:11,430 - vaxrank.core_logic:45 - INFO - No protein sequences for Variant(contig='17', start=1933381, ref='G', alt='A', reference_name='GRCh37')
2017-02-14 18:01:11,431 - isovar.allele_reads:200 - INFO - Gathering reads for Variant(contig='17', start=62502295, ref='C', alt='A', reference_name='GRCh37')
2017-02-14 18:01:11,461 - isovar.allele_reads:208 - INFO - Gathering variant reads for variant Variant(contig='17', start=62502295, ref='C', alt='A', reference_name='GRCh37') (chromosome = 17, gene names = ['DDX5'])
2017-02-14 18:01:11,528 - isovar.locus_reads:302 - INFO - Found 281 reads overlapping locus 17: 62502294-62502296
2017-02-14 18:01:11,528 - isovar.translation:453 - INFO - No supporting reads for variant Variant(contig='17', start=62502295, ref='C', alt='A', reference_name='GRCh37')
2017-02-14 18:01:11,529 - vaxrank.core_logic:45 - INFO - No protein sequences for Variant(contig='17', start=62502295, ref='C', alt='A', reference_name='GRCh37')
2017-02-14 18:01:11,529 - isovar.allele_reads:200 - INFO - Gathering reads for Variant(contig='17', start=62502324, ref='C', alt='A', reference_name='GRCh37')
2017-02-14 18:01:11,531 - isovar.allele_reads:208 - INFO - Gathering variant reads for variant Variant(contig='17', start=62502324, ref='C', alt='A', reference_name='GRCh37') (chromosome = 17, gene names = ['DDX5'])
2017-02-14 18:01:11,565 - isovar.locus_reads:302 - INFO - Found 266 reads overlapping locus 17: 62502323-62502325
2017-02-14 18:01:11,566 - isovar.variant_sequences:393 - INFO - Skipping Variant(contig='17', start=62502324, ref='C', alt='A', reference_name='GRCh37') because only 1 alt RNA reads (min=3)
2017-02-14 18:01:11,566 - isovar.translation:469 - INFO - No spanning cDNA sequences for variant Variant(contig='17', start=62502324, ref='C', alt='A', reference_name='GRCh37')
2017-02-14 18:01:11,566 - vaxrank.core_logic:45 - INFO - No protein sequences for Variant(contig='17', start=62502324, ref='C', alt='A', reference_name='GRCh37')
2017-02-14 18:01:13,712 - pyensembl.sequence_data:95 - INFO - Loaded sequence dictionary from /path/pyensembl-cache/pyensembl/GRCh37/ensembl75/Homo_sapiens.GRCh37.75.cdna.all.fa.gz.pickle
2017-02-14 18:01:14,229 - vaxrank.cli:253 - INFO - About to save args: {'vcf': ['/path/work/_v01_with-rna_Sample_-b37/6242eec0c3a2a65ba5ab136b38e3dcbe804f3995f0270bb58d58577fdc9cd8c3gatk_bqsred41b2cb5d309f5703c5aab75655d93agatk_bqsr_strelka-exome-defaultstrelka_output/results/passed_somatic_combined.vcf', '/path/work/_v01_with-rna_Sample_-b37/26160f7c5db17503fb83ea3d95da605c804f3995f0270bb58d58577fdc9cd8c3gatk_bqsred41b2cb5d309f5703c5aab75655d93agatk_bqsr_mutect-default-merged.vcf'], 'maf': [], 'variant': [], 'genome': None, 'json_variants': [], 'bam': '/path/work/_v01_with-rna_Sample_-b37/48c604cad7ad8816b58d4a92dc5fc521_path_work__v01_with-rna_Sample_-b37_9705c51188d8c1f95ef367a49e232df8_filtered_bamsamtoolsmerge.bam', 'min_mapping_quality': 1, 'use_duplicate_reads': False, 'drop_secondary_alignments': False, 'min_alt_rna_reads': 3, 'min_variant_sequence_coverage': 1, 'variant_sequence_assembly': True, 'protein_sequence_length': 20, 'max_reference_transcript_mismatches': 2, 'include_mismatches_after_variant': False, 'min_transcript_prefix_length': 10, 'mhc_predictor': 'netmhccons', 'mhc_epitope_lengths': [8, 9, 10, 11], 'mhc_alleles_file': '/path/work/_v01_with-rna_Sample_-b37/b84b8054b069332c2785ba004659c7ac8f71489687b19440ddcac1ce16a303f2rna0-_T_C2D8edsl-concatseq2hla-workdirhlarp.csv', 'mhc_alleles': '', 'vaccine_peptide_length': 25, 'padding_around_mutation': 5, 'max_vaccine_peptides_per_mutation': 3, 'max_mutations_in_report': 40, 'min_epitope_score': 0.001, 'output_patient_id': 'UNKNOWN', 'output_csv': '', 'output_ascii_report': '/path/work/_v01_with-rna_Sample_-b37/0d771abdf8f60720cf3495c56a50c73aepidisco-40pepnetmhcconsb84b8054b069332c2785ba004659c7ac8f71489687b19440ddcac1ce16a303f2rna0-_T_C2D8edsl-concatseq2hla-workdirhlarppassed_somatic_combinedvaxrank/vaxrank-result.txt', 'output_html_report': '', 'output_pdf_report': '/path/work/_v01_with-rna_Sample_-b37/0d771abdf8f60720cf3495c56a50c73aepidisco-40pepnetmhcconsb84b8054b069332c2785ba004659c7ac8f71489687b19440ddcac1ce16a303f2rna0-_T_C2D8edsl-concatseq2hla-workdirhlarppassed_somatic_combinedvaxrank/vaxrank-result.pdf', 'output_json_file': '', 'output_xlsx_report': '/path/work/_v01_with-rna_Sample_-b37/0d771abdf8f60720cf3495c56a50c73aepidisco-40pepnetmhcconsb84b8054b069332c2785ba004659c7ac8f71489687b19440ddcac1ce16a303f2rna0-_T_C2D8edsl-concatseq2hla-workdirhlarppassed_somatic_combinedvaxrank/vaxrank-result.xlsx', 'output_reviewed_by': '', 'output_final_review': '', 'cosmic_vcf_filename': ''}
Traceback (most recent call last):
  File "/nfs-pool/biokepi/toolkit/python-tools/envs/vaxrank.0.4.0/bin/vaxrank", line 11, in <module>
    sys.exit(main())
  File "/nfs-pool/biokepi/toolkit/python-tools/envs/vaxrank.0.4.0/lib/python3.6/site-packages/vaxrank/cli.py", line 302, in main
    csv_report_path=args.output_csv)
  File "/nfs-pool/biokepi/toolkit/python-tools/envs/vaxrank.0.4.0/lib/python3.6/site-packages/vaxrank/report.py", line 468, in make_csv_report
    all_dfs = pd.concat(frames.values())
  File "/nfs-pool/biokepi/toolkit/python-tools/envs/vaxrank.0.4.0/lib/python3.6/site-packages/pandas/tools/merge.py", line 1451, in concat
    copy=copy)
  File "/nfs-pool/biokepi/toolkit/python-tools/envs/vaxrank.0.4.0/lib/python3.6/site-packages/pandas/tools/merge.py", line 1484, in __init__
    raise ValueError('No objects to concatenate')
ValueError: No objects to concatenate