Error : read names of PET ends do not match[1] "removing duplicate PETs"

[ag-abhishek]

I have been encountering the error with my dataset set as well as with the sample dataset as mention in the supplementary material. I have tried my best to resolve it at my end and also with other guidance but failed each time.
It would be very kind if you help me to resolve the error or guide me with the possible change I can make to resolve this error

Here is the description of the input command, specification, and output when the Mango pipeline is used on the sample data as mentioned in the supplement for RAD21.

Command -

Rscript /mnt/raid/abhishek/software/mango/mango.R
--fastq1 /mnt/raid/abhishek/mango_sample/SNY_K562_RAD21_0.0_r1.fastq 
--fastq2 /mnt/raid/abhishek/mango_sample/SNY_K562_RAD21_0.0_r2.fastq 
--outdir /mnt/raid/abhishek/mango_sample/mango_output 
--bowtieref /mnt/raid/abhishek/software/bowtie1/index_hg19_ebt/hg19/hg19 
--bedtoolsgenome /mnt/raid/abhishek/software/bedtools2/genomes/human.hg19.genome 
--macs2path /mnt/raid/abhishek/software/MACS/bin/macs2 
--chromexclude chrM,chrY 
--reportallpairs TRUE 
--MACS_qvalue 0.05 
--stages 1:5

Specification -

Ubuntu - 18.04.5 LTS
Bowtie - version 1.3.0
Bedtools - bedtools v2.29.1
MACS2 - installed

OutPut -

Reported 168427037 alignments
[1] "score type detected: Sanger"
[1] "/mnt/raid/abhishek/software/bowtie1/bowtie-1.3.0-linux-x86_64/bowtie /mnt/raid/abhishek/software/bowtie1/index_hg19_ebt/hg19/hg19 /mnt/raid/abhishek/mango_sample/mango_output/mango_2.same.fastq /mnt/raid/abhishek/mango_sample/mango_output/mango_2.same.sam --phred33-quals -S -v 0 -k 1 --chunkmbs 500 --sam-nohead --mapq 40 -m 1 --threads 1"
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
# reads processed: 296761755
# reads with at least one alignment: 288518904 (97.22%)
# reads that failed to align: 8242851 (2.78%)
# reads with alignments suppressed due to -m: 120654005 (40.66%)
Reported 167864899 alignments
[1] "building bedpe"
Error: read names of PET ends do not match[1] "removing duplicate PETs"
Error: Can't subset columns that don't exist.
✖ Location 5 doesn't exist.
ℹ There are only 0 columns.
Backtrace:
     █
  1. └─mango::plotdistancedistribution(...)
  2.   ├─bedpe[, 5] /mnt/raid/abhishek/software/mango/R/plotdistancedistribution.R:8:2
  3.   └─tibble:::`[.tbl_df`(bedpe, , 5) /mnt/raid/abhishek/software/mango/R/plotdistancedistribution.R:8:2
  4.     └─tibble:::vectbl_as_col_location(...)
  5.       ├─tibble:::subclass_col_index_errors(...)
  6.       │ └─base::withCallingHandlers(...)
  7.       └─vctrs::vec_as_location(j, n, names)
  8.         └─(function () ...
  9.           └─vctrs:::stop_subscript_oob(...)
 10.             └─vctrs:::stop_subscript(...)
Execution halted
[mango.mango.log](https://github.com/dphansti/mango/files/5584509/mango.mango.log)

NOTE: I am also attaching the log file that shows the output (error) for your reference.

[ddduooo99]

Hi, may I ask how do you solve this question?