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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Error in hicpro2juicebox.sh process #301

Closed clementmo closed 3 years ago

clementmo commented 4 years ago

Dear Dr. Servant, Recently I am using hicpro2juicebox.sh to transfer allValidPairs to *.hic file. The code is as following: bash /public/home/lqiao/WPC/HiC-Pro_2.11.1/bin/utils/hicpro2juicebox.sh\ -i Ga_rep1.allValidPairs\ -g /public/home/lqiao/WPC/HiC-Pro_2.11.1/annotation/chrom_GhAt.size\ -j /public/home/lqiao/WPC/softwares/juicer/juicer_tools_1.14.08.jar\ -r /public/home/lqiao/WPC/HiC-Pro_2.11.1/annotation/HindIII_resfrag_GhAt.bed

The input files are in the following format: head -1 Ga_rep1.allValidPairs ##Lachesis_group0_ERROPOS100000 is the chr name, same in all related files. It was generated by HiC-pro-2.11, with each row in 12 columes.

Ga_Hi_C_rep1.340989953 Lachesis_group0_ERROPOS100000 12584 + Lachesis_group2_ERROPOS103218803 42135 - 452 HIC_Lachesis_group0_ERROPOS100000_2 HIC_Lachesis_group2_ERROPOS103218803_27 30 37

head -5 chrom_GhAt.size Lachesis_group10_ERROPOS100000 100000 Lachesis_group10_ERROPOS200000 100000 Lachesis_group10_ERROPOS300000 100000 Lachesis_group10_ERROPOS400000 100000 Lachesis_group10_ERROPOS500000 100000

head -5 HindIII_resfrag_GhAt.bed Lachesis_group10_ERROPOS100000 0 579 HIC_Lachesis_group10_ERROPOS100000_1 0 + Lachesis_group10_ERROPOS100000 579 1885 HIC_Lachesis_group10_ERROPOS100000_2 0 + Lachesis_group10_ERROPOS100000 1885 2726 HIC_Lachesis_group10_ERROPOS100000_3 0 + Lachesis_group10_ERROPOS100000 2726 3494 HIC_Lachesis_group10_ERROPOS100000_4 0 + Lachesis_group10_ERROPOS100000 3494 8496 HIC_Lachesis_group10_ERROPOS100000_5 0 +

juicer_tools_1.14.08.jar is the original file downloaded from https://github.com/aidenlab/juicer/wiki/Download .

It produced error: Running Juicebox ... Start preprocess Writing header Writing body .................................Error: the chromosome combination 5001_6138 appears in multiple blocks done !

I can't find 5001_6138 in the above files. What might be the problem? I need your help. Thank you so much.

Clement

nservant commented 4 years ago

Hi Clement, I just make a test with the latest Juicer tools version and it works well. It's difficult to help you without additional info ... N