duplicate 'names(reads)' not allowed

[lbwfff]

Dear Developer, I am having some problems running exomePeak2 analysis, here is my code:

library(exomePeak2)
gene_anno_gtf <- "/scratch/lb4489/bioindex/gencode.vM33.annotation.gtf"

input_files <- c('/scratch/lb4489/project/eem6a/ctrl_rep1.sorted.bam','/scratch/lb4489/project/eem6a/ctrl_rep2.sorted.bam','/scratch/lb4489/project/eem6a/ctrl_rep3.sorted.bam')
ip_files <- c('/scratch/lb4489/project/eem6a/ctrl_Merip_rep1.sorted.bam','/scratch/lb4489/project/eem6a/ctrl_Merip_rep2.sorted.bam','/scratch/lb4489/project/eem6a/ctrl_Merip_rep3.sorted.bam')
input_treated_files <- c('/scratch/lb4489/project/eem6a/treat_rep1.sorted.bam','/scratch/lb4489/project/eem6a/treat_rep2.sorted.bam','/scratch/lb4489/project/eem6a/treat_rep3.sorted.bam')  
ip_treated_files <- c('/scratch/lb4489/project/eem6a/treat_Merip_rep1.sorted.bam','/scratch/lb4489/project/eem6a/ctrl_Merip_rep2.sorted.bam','/scratch/lb4489/project/eem6a/treat_Merip_rep3.sorted.bam')

exomePeak2(bam_ip = ip_files, bam_input = input_files, 
           bam_ip_treated = ip_treated_files, bam_input_treated = input_treated_files, 
           gff = gene_anno_gtf, genome = "mm39", p_cutoff = 1e-2,
           experiment_name = paste0('exomePeak2_output_EE_vs_SH'))

Here is the output：

Extract bin features ... OK
Count reads on bin features ... Error in .local(features, reads, mode, ignore.strand, ...) : 
  duplicate 'names(reads)' not allowed
Calls: exomePeak2 ... featuresCounts -> summarizeOverlaps -> summarizeOverlaps -> .local
In addition: Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
Execution halted

Can you help me see what the problem is.

Thanks, LeeLee

[yuanjianwen-gif]

Hi, I have the same problem. How is it going?

[yuanjianwen-gif]

Guiding by https://www.biostars.org/p/119795/, I changed the IP/INPUT bam names, and it worked.