这个是hic pro得使用：
usage : HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v]Use option -h|--help for more informationHiC-Pro 3.1.0---------------OPTIONS ...
这个是hic pro得使用：
usage : HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v]
Use option -h|--help for more information
HiC-Pro 3.1.0
---------------
OPTIONS
-i|--input INPUT : input data folder; Must contains a folder per sample with input files
-o|--output OUTPUT : output folder
-c|--conf CONFIG : configuration file for Hi-C processing
[-p|--parallel] : if specified run HiC-Pro on a cluster
[-s|--step ANALYSIS_STEP] : run only a subset of the HiC-Pro workflow; if not specified the complete workflow is run
mapping: perform reads alignment - require fast files
proc_hic: perform Hi-C filtering - require BAM files
quality_checks: run Hi-C quality control plots
merge_persample: merge multiple inputs and remove duplicates if specified - require .validPairs files
build_contact_maps: Build raw inter/intrachromosomal contact maps - require .allValidPairs files
ice_norm : run ICE normalization on contact maps - require .matrix files
[-h|--help]: help
[-v|--version]: version
报错这一步是跑完了比对现在需要 pairing（R1/R2 配对）。也就是说在指定得out文件夹下面得bowtie_results/bwt2/sample/里面已经存在了R1和R2得bwt2merged.bam
报错原因：
R1和R2得bwt2merged.bam没有按照readname排序
可以通过这个查看到是否排序：
samtools view -H Asample_R1_genome.final.bwt2merged.bam | grep SO:
# @HD VN:1.0 SO:unsorted
解决方法：
重新排序后续跑
1. 排序：
cd out/bowtie_results/bwt2/sample/
mv sample_R1_genome.final.bwt2merged.bam sample_R1_genome.final.bwt2merged.bam.bck
mv sample_R2_genome.final.bwt2merged.bam sample_R2_genome.final.bwt2merged.bam.bck
samtools sort -n -@ 8 -o sample_R1_genome.final.bwt2merged.bam sample_R1_genome.final.bwt2merged.bam.bck
samtools sort -n -@ 8 -o sample_R2_genome.final.bwt2merged.bam sample_R2_genome.final.bwt2merged.bam.bck
2. 续跑：
cd ../../../../
HiC-Pro -i out/bowtie_results/bwt2/ -c ./config-hicpro.txt -o ./out -s proc_hic
两个注意点：
一个是-i指定输入文件夹一定是包含bam文件得那个文件夹，而不是最开始得data文件夹（包含fastq文件的那个）
一个是 -s需要proc_hic
