Sorted file and dups/no dups files do not add up in dedup step

[WeiCSong]

Hi, thanks for the great tool! i'm running juicer on a pair of hic fastq and everything went well until the dedup step

scripts/juicer.sh -t 4 -S dedup -p mygenome.chrom.sizes -z references/test_cpu_1.bp.p_ctg.fasta -y t2t_DpnII.txt
(-: Mark duplicates done successfully
***! Error! The sorted file and dups/no dups files do not add up, or were empty.

by samtools quickcheck, i found that the input aligned/merged_sort.bam and the output aligned/merged_dedup.sam are both intact and have no error, but they just did not add up. Also i did not receive any error message or summary file during the process. Do you have any suggestion on this issue? Thank you very much for your help.

[linxin1husky]

Similar things happened to me when I run the 2.0.0-beta version. I couldn't find any nodedup files in the aligned/ subfolder. ..

[ClaudioUPz]

This happened to me too, I ran version 2.20.00 and version 1.9.9 and it didn't generate either the sorted or nodups files, it did generate merged_dedup.bam but the program starts throwing errors after generating the .hic files