Encounter the error in cpsr-report-generation()

[A-Tsai]

I try to run the demo case, but failed to generate the report. Could you please help me to solve the problem?

cpsr \
     --input_vcf /home/azureuser/src/cpsr/examples/example.vcf.gz \
     --pcgr_dir /home/azureuser/src/pcgr-1.0.1 \
     --output_dir /home/azureuser/src/cpsr/output-cpsr \
     --genome_assembly grch37 \
     --panel_id 1 \
     --sample_id example \
     --no_docker \
     --maf_upper_threshold 0.2 \
     --force_overwrite

The error message:

...
2022-03-30 06:18:09 - cpsr-report-generation - INFO - Considering variants in the targeted predisposition genes: ACD, AIP, APC, ATM, BAP1, BMPR1A, BRAF, BRCA1, BRCA2, BRIP1, CBL, CDC73, CDH1, CDK4, CDKN1B, CDKN2A, CHEK2, CTC1, DDB2, DGCR8, DICER1, DKC1, EPCAM, ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, EXT1, EXT2, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FH, FLCN, HRAS, KIT, KRAS, LZTR1, MAP2K1, MAP2K2, MAX, MEN1, MET, MLH1, MSH2, MSH6, MUTYH, NF1, NF2, NOP10, NRAS, NTHL1, PALB2, PARN, PDGFRA, PMS2, POLD1, POLE, POLH, PPP1CB, PTCH1, PTEN, PTPN11, RABL3, RAD51C, RAD51D, RAF1, RB1, RET, RIT1, RTEL1, SDHA, SDHAF2, SDHB, SDHC, SDHD, SHOC2, SLX4, SMAD4, SMARCA4, SMARCB1, SOS1, SOS2, SPRED1, STK11, SUFU, TERC, TERT, TINF2, TMEM127, TP53, TSC1, TSC2, VHL, WRAP53, WT1, XPA, XPC
2022-03-30 06:18:09 - cpsr-report-generation - INFO - Total number of variants in target cancer predisposition genes (for TIER output): 38
2022-03-30 06:18:09 - cpsr-report-generation - INFO - Number of coding variants in target cancer predisposition genes (for TIER output): 21
2022-03-30 06:18:09 - cpsr-report-generation - INFO - Number of non-coding variants in cancer predisposition genes (for TIER output): 17
2022-03-30 06:18:09 - cpsr-report-generation - INFO - Generating tiered set of result variants for output in tab-separated values (TSV) file
2022-03-30 06:18:09 - cpsr-report-generation - INFO - Ignoring n = 0 unclassified variants with a global MAF frequency above 0.2
2022-03-30 06:18:09 - cpsr-report-generation - INFO - Merging ClinVar-classified variants and CPSR-classified (novel) variants - class1
2022-03-30 06:18:09 - cpsr-report-generation - INFO - Zero variants found - class1
2022-03-30 06:18:10 - cpsr-report-generation - INFO - Merging ClinVar-classified variants and CPSR-classified (novel) variants - class2
2022-03-30 06:18:10 - cpsr-report-generation - INFO - Merging ClinVar-classified variants and CPSR-classified (novel) variants - class3
2022-03-30 06:18:10 - cpsr-report-generation - INFO - Merging ClinVar-classified variants and CPSR-classified (novel) variants - class4
2022-03-30 06:18:10 - cpsr-report-generation - INFO - Merging ClinVar-classified variants and CPSR-classified (novel) variants - class5
2022-03-30 06:18:10 - cpsr-report-generation - INFO - Matching variant set with existing genomic biomarkers from CIViC (germline)
2022-03-30 06:18:10 - cpsr-report-generation - INFO - Found n = 0 clinical evidence item(s) at the exact level, 0 unique variant(s)
2022-03-30 06:18:10 - cpsr-report-generation - INFO - Found n = 0 clinical evidence item(s) at the codon level, 0 unique variant(s)
2022-03-30 06:18:10 - cpsr-report-generation - INFO - Found n = 0 clinical evidence item(s) at the exon level, 0 unique variant(s)
2022-03-30 06:18:10 - cpsr-report-generation - INFO - Found n = 3 clinical evidence item(s) at the gene level, 2 unique variant(s)
2022-03-30 06:18:10 - cpsr-report-generation - INFO - NF1:frameshift_variant:p.Pro678ArgfsTer10, CHEK2:splice_donor_variant:NA
2022-03-30 06:18:10 - cpsr-report-generation - INFO - Variants were found in the following cancer predisposition genes: PMS2, TP53, NF1, EPCAM, BRAF, POLE, SMARCA4, POLD1, CHEK2, APC, TSC1, TINF2, FANCA, SOS2, PARN, ERCC2, EXT1, MUTYH, PTEN, TSC2, SDHC, TERC, PDGFRA, KIT, CDKN2A, SDHD, BRCA2, MAP2K1, CDH1, ERCC1, AIP, RTEL1
2022-03-30 06:18:10 - cpsr-report-generation - INFO - ------
2022-03-30 06:18:10 - cpsr-report-generation - INFO - Writing SNV/InDel tab-separated output file with CPSR annotations - ('tsv')
2022-03-30 06:18:10 - cpsr-report-generation - INFO - ------
2022-03-30 06:18:10 - cpsr-report-generation - INFO - Writing JSON file (.json) with key report contents
Error in assertable::assert_colnames(report_strip$content$snv_indel$variant_set[[o]],  :
  These columns exist in colnames but not in your dataframe: EXONIC_STATUS DBSNPRSID COSMIC_MUTATION_ID CALL_CONFIDENCE DP_TUMOR AF_TUMOR DP_CONTROL AF_CONTROL TIER and these exist in your dataframe but not in colnames: VAR_ID GENOTYPE CPSR_CLASSIFICATION_SOURCE GENOME_VERSION VCF_SAMPLE_ID GENE_NAME CCDS UNIPROT_ID ENSEMBL_GENE_ID REFSEQ_MRNA VEP_ALL_CSQ REGULATORY_ANNOTATION DBSNP HGVSc LAST_EXON EXON_POSITION INTRON_POSITION CDS_CHANGE RMSK_HIT PROTEIN_FEATURE EFFECT_PREDICTIONS LOSS_OF_FUNCTION CANCER_PHENOTYPE CLINVAR_CLASSIFICATION CLINVAR_MSID CLINVAR_VARIANT_ORIGIN CLINVAR_CONFLICTED CLINVAR_PHENOTYPE CLINVAR_REVIEW_STATUS_STARS DBMTS miRNA_TARGET_HIT miRNA_TARGET_HIT_PREDICTION TF_BINDING_SITE_VARIANT TF_BINDING_SITE_VARIANT_INFO GERP_SCORE N_INSILICO_CALLED N_INSILICO_DAMAGING N_INSILICO_TOLERATED N_INSILICO_SPLICING_NEUTRAL N_INSILICO_SPLICING_AFFECTED GLOBAL_AF_GNOMAD NON_CANCER_AF_NFE ACMG_BA1_AD ACMG_BS1_1_AD ACMG_BS1_2_AD ACMG_BA1_AR ACMG_BS1_1_AR ACMG_BS1_2_AR AC
Calls: <Anonymous> -> <Anonymous>
Execution halted

[sigven]

Hi, thanks a lot for reporting. I will have a look today, I think I know the cause. Kind regards, Sigve

[sigven]

Hi @A-Tsai,

I have now fixed an issue in PCGR that was related to the JSON output crash in CPSR. You need to update PCGR to v.1.0.2, let me know if that is still causing issues for you.

kind regards, Sigve

[A-Tsai]

@sigven It works now. Many thanks.