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sgilab / JuLI

Junction Location Identifier (JuLI): DNA fusion detection tool for clinical sequencing.
GNU General Public License v3.0
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Error in bedDmerge[, c(1, 2, 3, which(grepl(paste0("_", m), colnames(bedDmerge))) #7

Open asaki1986 opened 4 years ago

asaki1986 commented 4 years ago

callfusion(CaseBam='/data/NGS/Ctdna-Data-Analysis/106.DataAnalysis/20200401_H33JCDSXY-P101SC18120363-01/analysis2/intermediate_bam/HO0327-GW9T0137B05_L2.raw_data_mapped.bam',TestI D='GW9T0137B05',OutputPath='../test/juli', Thread=20, Refgene='references/refGene_hg19.[2020-Jul-23 15:14:35] callfusion(CaseBam=/data/NGS/Ctdna-Data-Analysis/106.DataAnalysis/20200 401_H33JCDSXY-P101SC18120363-01/analysis2/intermediate_bam/HO0327-GW9T0137B05_L2.raw_data_mapped.bam,ControlBam=NULL,TestID=GW9T0137B05,OutputPath=../test/juli,Thread=20,ControlPane l=NULL,TargetBed=NULL,Refgene=references/refGene_hg19.txt,Gap=references/gap_hg19.txt,Reference=/bioinfo/data/Genomes/NCBI/build37/Sequence/WholeGenomeFasta/human_g1kv37.fasta,Anal ysisType=DP,AnalysisUnit=1000,MinMappingQuality=0,SplitCutoff=2,DiscordantCutoff=3,NucDiv=TRUE,SplitRatio=0.7,MatchBase=10,Log=FALSE) [2020-Jul-23 15:14:35] JuLI v0.1.6 [2020-Jul-23 15:14:35] Measuring bam statistics [2020-Jul-23 15:14:38] Identifying candidate breaks [2020-Jul-23 15:15:14] Analysing discordant pairs [2020-Jul-23 15:15:14] -Counting supporting reads [2020-Jul-23 15:18:13] -Generating consensus contigs [2020-Jul-23 15:18:35] -Comparing contigs between breaks [2020-Jul-23 15:18:52] Analysing proper pairs [2020-Jul-23 15:18:52] -Counting supporting reads [2020-Jul-23 15:19:57] -Generating consensus contigs [2020-Jul-23 15:24:33] -Comparing contigs between breaks Error in bedDmerge[, c(1, 2, 3, which(grepl(paste0("", m), colnames(bedDmerge))), : incorrect number of dimensions

Hi,

I used callfusion command to evaluate the fusion status of bam file. However, error messages came out during calling process.

Any method to fix the issue?

Thanks, Junfeng

nvolkovaGEL commented 4 years ago

Hi Junfeng, Sorry to interfere, but I also had this issue once my "vctrs" R package got updated beyond 0.2.2 version. It disappeared when I reverted back to v.0.2.2. May that could help you as well!