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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
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Sorted file and dups/no dups files do not add up in dedup step #345

Open WeiCSong opened 9 months ago

WeiCSong commented 9 months ago

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 commented 7 months ago

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. ..