Error in collapse(tmp, inner = FALSE, indent = indent) : R character strings are limited to 2^31-1 bytes

[jxshi]

Hi @sigven ,

Thank for your cpsr and pcgr software. I have used pcgr for a while and I love it. I tried cpsr today and successfully tested the example vcf file. When I tried to use my own data, and it pops up the following error message. Can you check for me please? Thank you in advance!

ERROR message:

2019-01-27 00:32:06 - cpsr-writer - INFO - STEP 4: Generation of output files - Cancer predisposition sequencing report
2019-01-26 16:32:35 [INFO] Excluding 0 variants from non-nuclear chromosomes/scaffolds
2019-01-26 16:32:36 [INFO] Number of PASS variants: 318
2019-01-26 16:32:36 [INFO] Number of SNVs: 288
2019-01-26 16:32:36 [INFO] Number of deletions: 26
2019-01-26 16:32:36 [INFO] Number of insertions: 4
2019-01-26 16:32:36 [INFO] Number of block substitutions: 0
2019-01-26 16:32:36 [INFO] Extending annotation descriptions related to UniprotKB/SwissProt protein features
2019-01-26 16:32:37 [INFO] Adding citations/phenotypes underlying GWAS hits (NHGRI-EBI GWAS Catalog)
2019-01-26 16:32:37 [INFO] Extending annotation descriptions related to Database of Curated Mutations (DoCM)
2019-01-26 16:32:38 [INFO] Extending annotation descriptions related to KEGG pathways
2019-01-26 16:32:38 [INFO] Extending annotation descriptions related to ClinVar
2019-01-26 16:32:41 [INFO] Filtering variants against the predefined list of n = 209 cancer predisposition genes
2019-01-26 16:32:41 [INFO] Number of variants within cancer predisposition genes: 262
2019-01-26 16:32:41 [INFO] Number of coding variants in cancer predisposition genes: 80
2019-01-26 16:32:41 [INFO] Found coding variants in the following cancer predisposition genes: KIF1B, MUTYH, ERCC3, CXCR4, MLH1, GATA2, FAT1, SDHA, PRDM9, MSH3, RAD50, NSD1, PRSS1, WRN, TSC1, RET, JMJD1C, FANCF, FEN1, CDKN1B, SH2B3, HNF1A, POLE, SERPINA1, BLM, TERF2IP, FANCA, NF1, HNF1B, BRCA1, POLD1, APOBEC3B
2019-01-26 16:32:41 [INFO] Looking up germline variants linked to hereditary cancer-predisposing syndromes/cancer phenotypes
2019-01-26 16:32:41 [INFO] Assignment of variants to tier 1/tier 2/tier 3
2019-01-26 16:32:41 [INFO] TIER 1: Pathogenic variants - cancer_phenotype: n = 2
2019-01-26 16:32:41 [INFO] TIER 1: Pathogenic variants - noncancer_phenotype: n = 2
2019-01-26 16:32:41 [INFO] TIER 2: Likely pathogenic variants - cancer_phenotype: n = 0
2019-01-26 16:32:41 [INFO] TIER 2: Likely pathogenic variants - noncancer_phenotype: n = 0
2019-01-26 16:33:08 [INFO] TIER 3: Variants of uncertain significance - cancer_phenotype: n = 131088
2019-01-26 16:33:09 [INFO] TIER 3: Variants of uncertain significance - noncancer_phenotype: n = 2
2019-01-26 16:35:32 [INFO] TIER 3: Other unclassified variants: n = 1376306
2019-01-26 16:35:32 [INFO] Generating tiered set of result variants for output in tab-separated values (TSV) file
Error in collapse(tmp, inner = FALSE, indent = indent) :
  R character strings are limited to 2^31-1 bytes
Calls: <Anonymous> ... vapply -> FUN -> FUN -> .local -> collapse -> .Call
Execution halted

Best regards,

Jianxiang

[sigven]

Dear Jianxiang, Thanks a lot for reporting this! Would it be possible for you to share your input, as this is the likely cause for the bug (an un-anticipated type of input somewhere)? regards, Sigve

[jxshi]

Hi Sigve,

Here is the link to the vcf file that I used. I tried on two different severs and both failed with the same error. By the way, the shared link will expire in 7 days.

Thank you for you time!

All the best,

Jianxiang

[sigven]

Hi,

FYI: the VCF being linked is a VCF file with somatic calls (tumor sample + normal sample), i.e. as used for PCGR. CPSR requires germline calls as input.

[jxshi]

Hi,

Thank you for pointing that out. I will try later with germline VCF file.

Cheers!

Jianxiang

[xiaoqiwang19]

Has this problem been solved ? I had the same problem.