error when run JuLI-v0.1.6.2

[zhangshouwei309194]

Dear author:
When i ran juli, i met some questions. the description is as follows:

command:
Rscript juli.fusion.R JuLI_test.bam test outdir 1 refdir hg19.fa
juli.fusion.R:
library(juliv0.1.6.2)

args = commandArgs(trailingOnly=TRUE)

bam <- args[1]
prefix <- args[2]
odir <- args[3]
thread <- args[4]
refdir <- args[5]
genome <- args[6]

callfusion(CaseBam=bam,
TestID=prefix,
OutputPath=odir,
Thread=thread,
Refgene=paste(refdir,'refGene_hg19.txt',sep='/'),
Gap=paste(refdir,'gap_hg19.txt',sep='/'),
Reference=genome)

out <- paste(prefix,'JuLI_fusion.txt',sep='.')

annofusion(Output=paste(odir,out,sep='/'),
Refgene=paste(refdir,'refGene_hg19.txt',sep='/'),
Cosmic=paste(refdir,'CosmicFusionExport_V76.tsv',sep='/'),
Pfam=paste(refdir,'Pfam-A.full.human',sep='/')
Uniprot=paste(refdir,'HGNC_GeneName_UniProtID_160524.txt',sep='/'))

issue:
[2023-Jul-04 17:32:35] callfusion(CaseBam=JuLI_test.bam,ControlBam=NULL,TestID=test,OutputPath=/home/swzhang/software/JuLI/JuLI-v0.1.6.2/test,Thread=1,ControlPanel=NULL,TargetBed=NULL,Refgene=/home/swzhang/software/JuLI/JuLI-v0.1.6.2/references/refGene_hg19.txt,Gap=/home/swzhang/software/JuLI/JuLI-v0.1.6.2/references/gap_hg19.txt,Reference=/ifs3/qyzuo/Cancer/database/hg19/hg19.fa,AnalysisType=DP,AnalysisUnit=1000,MinMappingQuality=0,SplitCutoff=2,DiscordantCutoff=3,NucDiv=TRUE,AlignmentNumber=6,SplitRatio=0.7,MatchBase=10,Log=FALSE)
[2023-Jul-04 17:32:35] JuLI v0.1.6
[2023-Jul-04 17:32:35] Measuring bam statistics
[2023-Jul-04 17:32:36] Identifying candidate breaks
[2023-Jul-04 17:32:37] Analysing discordant pairs
[2023-Jul-04 17:32:37] -Counting supporting reads
Error in { :
task 3 failed - "'list' object cannot be coerced to type 'double'"
Calls: callfusion ... %>% -> filter -> rbindlist -> %dopar% ->
Execution halted

  My R's version  is 4.2.1. Could you please provide me some clues？Look foward to your reply!

Yours sincerely
Phillip

[bioxu]

Hi, @zhangshouwei309194, did you find a solution to this problem? I'm also meet the same question.

[yaowei2010]

Hello, I also got the similar error on the problem. And I also install the package with 0.1.6.2 version.