Bug: `object 'RMSK_HIT' not found`

[vladsavelyev]

Hi Sigve,

Thanks for promptly fixing CPSR bugs. I got another one for you, below' the log:

cpsr.py --input_vcf SFRC01085__PRJ180621_SFRC01085-1MT-normal.vcf.gz pcgr . grch37 cpsr.toml SFRC01085__PRJ180621_SFRC01085-1MT-normal  --docker-uid root --force_overwrite
2018-11-16 12:06:07 - cpsr-validate-input - INFO - STEP 0: Validate input data
2018-11-16 01:06:13 - cpsr-validate-input - INFO - Skipping validation of VCF file - as defined in configuration file (vcf_validation = false)
2018-11-16 01:06:13 - cpsr-validate-input - INFO - Checking if existing INFO tags of query VCF file coincide with CPSR INFO tags
2018-11-16 01:06:13 - cpsr-validate-input - INFO - No query VCF INFO tags coincide with CPSR INFO tags
2018-11-16 12:06:10 - cpsr-validate-input - INFO - Finished

2018-11-16 12:06:10 - cpsr-vep - INFO - STEP 1: Basic variant annotation with Variant Effect Predictor (94, GENCODE release 19, grch37) including loss-of-function prediction
2018-11-16 12:08:46 - cpsr-vep - INFO - Finished

2018-11-16 12:08:46 - cpsr-vcfanno - INFO - STEP 2: Annotation for cancer predisposition with cpsr-vcfanno (ClinVar, dbNSFP, UniProtKB, cancerhotspots.org, GWAS catalog)
2018-11-16 12:09:01 - cpsr-vcfanno - INFO - Finished

2018-11-16 12:09:01 - cpsr-summarise - INFO - STEP 3: Cancer gene annotations with cpsr-summarise
2018-11-16 01:09:07 - cpsr-gene-annotate - INFO - Completed summary of functional annotations for 954 variants on chromosome 1
...
2018-11-16 01:09:15 - cpsr-gene-annotate - INFO - Number of non-PASS/REJECTED variant calls: 0
2018-11-16 01:09:15 - cpsr-gene-annotate - INFO - Number of PASSed variant calls: 26157
2018-11-16 12:09:15 - cpsr-summarise - INFO - Converting VCF to TSV with https://github.com/sigven/vcf2tsv
2018-11-16 12:09:39 - cpsr-summarise - INFO - Finished

2018-11-16 12:09:39 - cpsr-writer - INFO - STEP 4: Generation of output files - Cancer predisposition sequencing report
^[[I^[[O^[[I^[[O^[[I^[[O^[[I^[[O2018-11-16 01:10:17 [INFO] Excluding 0 variants from non-nuclear chromosomes/scaffolds
2018-11-16 01:10:19 [INFO] Number of PASS variants: 26157
2018-11-16 01:10:20 [INFO] Number of SNVs: 20933
2018-11-16 01:10:20 [INFO] Number of deletions: 2650
2018-11-16 01:10:20 [INFO] Number of insertions: 2574
2018-11-16 01:10:20 [INFO] Number of block substitutions: 0
2018-11-16 01:10:20 [INFO] Extending annotation descriptions related to UniprotKB/SwissProt protein features
2018-11-16 01:10:22 [INFO] Adding citations/phenotypes underlying GWAS hits (NHGRI-EBI GWAS Catalog)
2018-11-16 01:10:23 [INFO] Extending annotation descriptions related to Database of Curated Mutations (DoCM)
2018-11-16 01:10:24 [INFO] Extending annotation descriptions related to KEGG pathways
2018-11-16 01:10:26 [INFO] Extending annotation descriptions related to ClinVar
2018-11-16 01:10:37 [INFO] Filtering variants against the predefined list of n = 209 cancer predisposition genes
2018-11-16 01:10:38 [INFO] Number of variants within cancer predisposition genes: 23096
2018-11-16 01:10:38 [INFO] Number of coding variants in cancer predisposition genes: 91
2018-11-16 01:10:38 [INFO] Found coding variants in the following cancer predisposition genes: SPRTN, ALK, MSH6, ABCB11, BARD1, FANCD2, MLH1, POLQ, CASR, GATA2, ATR, KIT, PTPN13, FAT1, SDHA, DROSHA, MSH3, APC, HFE, PMS2, PRSS1, WRN, NBN, DOCK8, PTCH1, TGFBR1, JMJD1C, BMPR1A, CDKN1C, MEN1, AIP, CEP57, ATM, SH2B3, HNF1A, POLE, BRCA2, ERCC5, RAD51B, MLH3, SERPINA1, BUB1B, FAH, FANCI, TSC2, ACD, RFWD3, TP53, BRIP1, AXIN2, RHBDF2, SETBP1, SMARCA4, ERCC2, APOBEC3B, AR
2018-11-16 01:10:38 [INFO] Looking up germline variants linked to hereditary cancer-predisposing syndromes/cancer phenotypes
2018-11-16 01:10:41 [INFO] Assignment of variants to tier 1/tier 2/tier 3
2018-11-16 01:10:41 [INFO] TIER 1: Pathogenic variants - cancer_phenotype: n = 0
2018-11-16 01:10:41 [INFO] TIER 1: Pathogenic variants - noncancer_phenotype: n = 1
2018-11-16 01:10:41 [INFO] TIER 2: Likely pathogenic variants - cancer_phenotype: n = 0
2018-11-16 01:10:41 [INFO] TIER 2: Likely pathogenic variants - noncancer_phenotype: n = 0
2018-11-16 01:10:41 [INFO] TIER 3: Variants of uncertain significance - cancer_phenotype: n = 13
2018-11-16 01:10:43 [INFO] TIER 3: Variants of uncertain significance - noncancer_phenotype: n = 4
Error in `[.data.frame`(cpg_calls, !is.na(cpg_calls$CONSEQUENCE) & is.na(RMSK_HIT) &  :
  object 'RMSK_HIT' not found
Calls: <Anonymous> -> <Anonymous> -> nrow -> [ -> [.data.frame
Execution halted

The VCF and toml are attached in an archive: vlad_cpsr_bug.zip

Vlad

[sigven]

Should be fixed now, new release and bundle. Thanks for bug reporting, again :-)