Error in .f(.x[[i]], ...) : object 'ts_oncogene' not found

[vladsavelyev]

Hey Sigve,

Testing the most recent codebase (normal dockerized install). I updated the dev image and downloaded the most recent data bundle, running an example and getting this errror:

python pcgr.py --input_vcf examples/tumor_sample.COAD.vcf.gz --input_cna examples/tumor_sample.COAD.cna.tsv . examples grch37 examples/pcgr_conf.COAD.toml tumor_sample.COAD
...
2018-10-29 03:28:57 [INFO] Calculating tumor mutational burden
2018-10-29 03:28:58 [INFO] Number of variants for mutational burden analysis: 2709
2018-10-29 03:28:58 [INFO] Estimated mutational burden: 75.25 mutations/Mb
2018-10-29 03:28:58 [INFO] Mutational burden tertile: TMB - High ( > 20 mutations/Mb)
2018-10-29 03:28:58 [INFO] ------
2018-10-29 03:28:58 [INFO] ------
2018-10-29 03:28:58 [INFO] Generating report data for copy number segment file /workdir/input_cna/tumor_sample.COAD.cna.tsv
Error in .f(.x[[i]], ...) : object 'ts_oncogene' not found
Calls: <Anonymous> ... <Anonymous> -> vars_select_eval -> map_if -> map -> .Call -> .f
Execution halted

[pdiakumis]

Debugging the pcgrr::generate_report_data_cna function, it looks like the ts_oncogene column isn't in the pcgr_data$gencode_genes_gr list, so it can't find it when doing dplyr::select so errors out. Not sure if we need that column. There are two similarly named columns, tsgene and p_oncogene in the ranges object:

  ranges <- pcgr_data$gencode_genes_gr[subjectHits(hits)]
  mcols(ranges) <- c(mcols(ranges),mcols(cna_gr[queryHits(hits)]))

  local_df <- as.data.frame(mcols(ranges))
  local_df$segment_start <- start(ranges(cna_gr[queryHits(hits)]))
  local_df$segment_end <- end(ranges(cna_gr[queryHits(hits)]))
  local_df$segment_length_Mb <- round((as.numeric((local_df$segment_end - local_df$segment_start)/1000000)),digits = 4)

  local_df$transcript_start <- start(ranges)
  local_df$transcript_end <- end(ranges)
  local_df$chrom <- as.character(seqnames(ranges))
  local_df <- as.data.frame(local_df %>% dplyr::rowwise() %>% dplyr::mutate(transcript_overlap_percent = round(as.numeric((min(transcript_end,segment_end) - max(segment_start,transcript_start)) / (transcript_end - transcript_start)) * 100, digits = 2)))
  local_df$segment_link <- paste0("<a href='",paste0(ucsc_browser_prefix,paste0(local_df$chrom,':',local_df$segment_start,'-',local_df$segment_end)),"' target=\"_blank\">",paste0(local_df$chrom,':',local_df$segment_start,'-',local_df$segment_end),"</a>")

  local_df_print <- local_df
  local_df_print <- dplyr::select(local_df_print,chrom,segment_start,segment_end,segment_length_Mb,
                                  event_type,cytoband,LogR,ensembl_gene_id,symbol,ensembl_transcript_id,
                                  transcript_start,transcript_end,transcript_overlap_percent,name,biotype,
                                  disgenet_cui,tsgene,intogen_drivers,chembl_compound_id,
                                  gencode_gene_biotype,gencode_tag,gencode_release)
...
...
object 'ts_oncogene' not found

> names(mcols(ranges))
 [1] "ensembl_gene_id"            "symbol"                     "gencode_gene_biotype"       "gencode_tag"                "biotype"
 [6] "ensembl_transcript_id"      "ensembl_transcript_id_full" "gencode_release"            "name"                       "entrezgene"
[11] "principal_isoform_flag"     "uniprot_acc"                "uniprot_id"                 "corum_id"                   "MIM_id"
[16] "MIM_phenotype_id"           "tsgene"                     "p_oncogene"                 "disgenet_cui"               "predisp_source"
[21] "predisp_cancer_cui"         "predisp_cancer_moi"         "predisp_syndrome_cui"       "intogen_drivers"            "tcga_driver"
[26] "chembl_compound_id"         "oncoscore"                  "ncg"                        "Sample"                     "Num_Probes"
[31] "LogR"                       "segmentID"                  "cytoband"                   "event_type"

[sigven]

Hi Peter and Vlad,
Thanks, forgot testing this. You are correct, Peter. It's the oncogene that has been changed. I'll fix this asap.

[sigven]

You can re-try now.

[vladsavelyev]

Awesome, thanks Sigve, it works now! PCGR creates the report even though it prints some errors in the end which I'm not sure if affect anything:

2018-10-30 21:40:11 [INFO] Rendering HTML report with rmarkdown
Warning messages:
1: In instance$preRenderHook(instance) :
  It seems your data is too big for client-side DataTables. You may consider server-side processing: https://rstudio.github.io/DT/server.html
2: In replayPlot(x) : graphical parameter "cin" cannot be set
3: In replayPlot(x) : graphical parameter "cra" cannot be set
4: In replayPlot(x) : graphical parameter "csi" cannot be set
5: In replayPlot(x) : graphical parameter "cxy" cannot be set
6: In replayPlot(x) : graphical parameter "din" cannot be set
7: In replayPlot(x) : graphical parameter "page" cannot be set
8: In file.rename(from, to) :
  cannot rename file '/data/cephfs/punim0010/extras/vlad/synced/pcgr/examples/output/tumor_sample.COAD.pcgr_acmg.grch37_files/figure-html' to '/data/cephfs/punim0010/extras/vlad/synced/pcgr/examples/output//data/cephfs/punim0010/extras/
vlad/synced/pcgr/examples/output/tumor_sample.COAD.pcgr_acmg.grch37_files/figure-html', reason 'No such file or directory'
9: In file.rename(from, to) :
  cannot rename file '/data/cephfs/punim0010/extras/vlad/synced/pcgr/examples/output//data/cephfs/punim0010/extras/vlad/synced/pcgr/examples/output/tumor_sample.COAD.pcgr_acmg.grch37_files/figure-html' to '/data/cephfs/punim0010/extras/
vlad/synced/pcgr/examples/output/tumor_sample.COAD.pcgr_acmg.grch37_files/figure-html', reason 'No such file or directory'
2018-10-30 21:41:10 - pcgr-writer - INFO - Finished

This is the no-docker version, so might have something to do with the installation? But the report looks good.

[sigven]

I actually see the same errors (warnings actually) when I run the report generation locally, I believe the graphical stuff comes from deconstructSigs, while the latter comes from the markdown report engine. Report is always generated, but one day I'll have to try getting rid of these warnings :-)