##HiC-Pro mapping : does not exist or is not a Bowtie 2 index

Hi,** would you please help me figure out where the errors are ? Any suggestions woluld be appreciated.

Here is directory hierarchy : under the directory `index`, `hg19` was downloaded form here index . And `hg19_bt2` was generated manually using `bowtie2` on my laptop. But both does not work.

. ├── annotation │ ├── hg19.chrom.sizes │ └── hg19_hindiii.bed ├── config-hicpro.txt ├── hicpro_test │ ├── bowtie_results │ │ └── bwt2_global │ │ └── dixon_2M_2 │ ├── config-hicpro.txt │ ├── logs │ │ └── dixon_2M_2 │ │ ├── mapping_step1.log │ │ ├── SRR400264_01_R1_bowtie2.log │ │ └── SRR400264_01_R2_bowtie2.log │ ├── rawdata -> /home/HICPRO/input/test_dataset/rawdata/ │ └── tmp ├── index │ ├── hg19 │ │ ├── hg19.1.bt2 │ │ ├── hg19.2.bt2 │ │ ├── hg19.3.bt2 │ │ ├── hg19.4.bt2 │ │ ├── hg19.rev.1.bt2 │ │ └── hg19.rev.2.bt2 │ └── hg19_bt2 │ ├── hg19.1.bt2 │ ├── hg19.2.bt2 │ ├── hg19.3.bt2 │ ├── hg19.4.bt2 │ ├── hg19.rev.1.bt2 │ └── hg19.rev.2.bt2 ├── rawdata │ ├── dixon_2M │ │ ├── SRR400264_00_R1.fastq.gz │ │ └── SRR400264_00_R2.fastq.gz │ └── dixon_2M_2 │ ├── SRR400264_01_R1.fastq.gz │ └── SRR400264_01_R2.fastq.gz └── reference └── hg19.fa

Here is the `config.txt` :

`# Please change the variable settings below if necessary

#########################################################################

Paths and Settings - Do not edit !

#########################################################################

TMP_DIR = tmp LOGS_DIR = logs BOWTIE2_OUTPUT_DIR = bowtie_results MAPC_OUTPUT = hic_results RAW_DIR = rawdata

#######################################################################

SYSTEM AND SCHEDULER - Start Editing Here !!

####################################################################### N_CPU = 4 SORT_RAM = 8192M LOGFILE = hicpro.log

JOB_NAME = JOB_MEM = JOB_WALLTIME = JOB_QUEUE = JOB_MAIL =

#########################################################################

Data

######################################################################### PAIR1_EXT = _R1 PAIR2_EXT = _R2

#######################################################################

Alignment options

#######################################################################

MIN_MAPQ = 10

BOWTIE2_IDX_PATH = /home/HICPRO/input/test_dataset/index/hg19_bt2/ BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder BOWTIE2_LOCAL_OPTIONS = --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder

#######################################################################

Annotation files

#######################################################################

REFERENCE_GENOME =/home/HICPRO/input/test_dataset/reference/hg19.fa GENOME_SIZE =/home/HICPRO/input/test_dataset/annotation/hg19.chrom.sizes #######################################################################

Allele specific analysis

#######################################################################

ALLELE_SPECIFIC_SNP =

#######################################################################

Capture Hi-C analysis

#######################################################################

CAPTURE_TARGET = REPORT_CAPTURE_REPORTER = 1

#######################################################################

Digestion Hi-C

#######################################################################

GENOME_FRAGMENT =/home/HICPRO/input/test_dataset/annotation/hg19_hindiii.bed LIGATION_SITE = AAGCTAGCTT MIN_FRAG_SIZE = MAX_FRAG_SIZE = MIN_INSERT_SIZE = MAX_INSERT_SIZE = "config-hicpro.txt" 98L, 3094C `

Here is the error information :

[root@localhost test_dataset]# time /usr/local/bin/HiC-Pro_3.0.0/bin/HiC-Pro -c config-hicpro.txt -i rawdata/ -o hicpro_test

Run HiC-Pro 3.0.0

Sun Mar 14 23:14:17 EDT 2021 Bowtie2 alignment step1 ... Logs: logs/dixon_2M_2/mapping_step1.log /usr/local/bin//HiC-Pro_3.0.0/scripts/hic.inc.sh: line 86: bowtie_results/bwt2_global/dixon_2M_2/SRR400264_01R1/home/HICPRO/input/test_dataset/reference/hg19.fa.bwt2glob.bam: No such file or directory /usr/local/bin//HiC-Pro_3.0.0/scripts/hic.inc.sh: line 86: bowtie_results/bwt2_global/dixon_2M_2/SRR400264_01R2/home/HICPRO/input/test_dataset/reference/hg19.fa.bwt2glob.bam: No such file or directory Exit: Error in reads alignment - Exit make: *** [/usr/local/bin/HiC-Pro_3.0.0/bin/../scripts//Makefile:88: bowtie_global] Error 1

real 0m4.093s user 0m0.255s sys 0m0.304s `

here is the log :

`[root@localhost test_dataset]# cat hicpro_test/logs/dixon_2M_2/SRR400264_01_R1_bowtie2.log

HiC-Pro mapping

(ERR): "/home/HICPRO/input/test_dataset/index/hg19_bt2///home/HICPRO/input/test_dataset/reference/hg19.fa" does not exist or is not a Bowtie 2 index Exiting now ... [root@localhost test_dataset]# cat hicpro_test/logs/dixon_2M_2/SRR400264_01_R2_bowtie2.log

HiC-Pro mapping

(ERR): "/home/HICPRO/input/test_dataset/index/hg19_bt2///home/HICPRO/input/test_dataset/reference/hg19.fa" does not exist or is not a Bowtie 2 index Exiting now ... `

thank you

nservant / HiC-Pro