problem first user

[robeach78]

sudo /usr/local/bin/HiC-Pro_3.0.0/bin/HiC-Pro -i mydata -o prova -c config-hicpro.txt

Run HiC-Pro 3.0.0

Thu Mar 4 13:28:01 CET 2021 Bowtie2 alignment step1 ... Logs: logs/sample1/mapping_step1.log Exit: Error in reads alignment - Exit make: *** [/usr/local/bin/HiC-Pro_3.0.0/bin/../scripts//Makefile:88: bowtie_global] Error 1

CONFIG FILE:

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 = 2 SORT_RAM = 1000M LOGFILE = hicpro.log

JOB_NAME = CTCF JOB_MEM = 10gb JOB_WALLTIME = 6:00:00 JOB_QUEUE = batch JOB_MAIL = roberto.ferrari@crg.es

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

Data

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

PAIR1_EXT = _R1 PAIR2_EXT = _R2

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

Alignment options

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

MIN_MAPQ = 10

BOWTIE2_IDX_PATH = /Users/RobertoFerrari/Downloads/bowtie_indexes/ 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 = hg38 GENOME_SIZE = hg38.genome

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

Allele specific analysis

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

ALLELE_SPECIFIC_SNP =

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

Capture Hi-C analysis

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

CAPTURE_TARGET = REPORT_CAPTURE_REPORTER = 1

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

Digestion Hi-C

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

GENOME_FRAGMENT = LIGATION_SITE = MIN_FRAG_SIZE = MAX_FRAG_SIZE = MIN_INSERT_SIZE = MAX_INSERT_SIZE =

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

Hi-C processing

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

MIN_CIS_DIST = GET_ALL_INTERACTION_CLASSES = 1 GET_PROCESS_SAM = 0 RM_SINGLETON = 1 RM_MULTI = 1 RM_DUP = 1

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

Contact Maps

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

BIN_SIZE = 20000 40000 150000 500000 1000000 MATRIX_FORMAT = upper

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

Normalization

####################################################################### MAX_ITER = 100 FILTER_LOW_COUNT_PERC = 0.02 FILTER_HIGH_COUNT_PERC = 0 EPS = 0.1

[robeach78]

here the log:

/Applications/anaconda3/bin/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/sample1/HiChiP_CTCF_2M_R2_hg38.bwt2glob.unmap.fastq --rg-id BMG --rg SM:HiChiP_CTCF_2M_R2 -p 1 -x /Users/RobertoFerrari/Downloads/bowtie_indexes//hg38 -U rawdata/sample1/HiChiP_CTCF_2M_R2.fastq.gz 2>> logs/sample1/HiChiP_CTCF_2M_R2_bowtie2.log> bowtie_results/bwt2_global/sample1/HiChiP_CTCF_2M_R2_hg38.bwt2glob.bam /Applications/anaconda3/bin/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/sample1/HiChiP_CTCF_2M_R1_hg38.bwt2glob.unmap.fastq --rg-id BMG --rg SM:HiChiP_CTCF_2M_R1 -p 1 -x /Users/RobertoFerrari/Downloads/bowtie_indexes//hg38 -U rawdata/sample1/HiChiP_CTCF_2M_R1.fastq.gz 2>> logs/sample1/HiChiP_CTCF_2M_R1_bowtie2.log> bowtie_results/bwt2_global/sample1/HiChiP_CTCF_2M_R1_hg38.bwt2glob.bam

[robeach78]

when I try to run the command:

(base) ➜ HiC-Pro-master /Applications/anaconda3/bin/bowtie2 dyld: Library not loaded: @rpath/libtbb.dylib Referenced from: /Applications/anaconda3/bin/bowtie2-align-s Reason: image not found (ERR): Description of arguments failed! Exiting now ...

[robeach78]

bowtie2 index:

/Users/RobertoFerrari/Downloads/bowtie_indexes (base) ➜ bowtie_indexes ls hg38.1.bt2 hg38.2.bt2 hg38.3.bt2 hg38.4.bt2 hg38.rev.1.bt2 hg38.rev.2.bt2

[robeach78]

log:

HiC-Pro mapping

dyld: Library not loaded: @rpath/libtbb.dylib Referenced from: /Applications/anaconda3/bin/bowtie2-align-s Reason: image not found (ERR): Description of arguments failed! Exiting now ... HiChiP_CTCF_2M_R1_bowtie2.log (END)

[nservant]

Hi, Thanks for all the logs. To me, this is a pure bowtie2 issue.

If you simply run the command ;

/Applications/anaconda3/bin/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/sample1/HiChiP_CTCF_2M_R2_hg38.bwt2glob.unmap.fastq --rg-id BMG --rg SM:HiChiP_CTCF_2M_R2 -p 1 -x /Users/RobertoFerrari/Downloads/bowtie_indexes//hg38 -U rawdata/sample1/HiChiP_CTCF_2M_R2.fastq.gz 2>> logs/sample1/HiChiP_CTCF_2M_R2_bowtie2.log> bowtie_results/bwt2_global/sample1/HiChiP_CTCF_2M_R2_hg38.bwt2glob.bam

does it work ?

[robeach78]

no it does not:

/Applications/anaconda3/bin/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/sample1/HiChiP_CTCF_2M_R2_hg38.bwt2glob.unmap.fastq --rg-id BMG --rg SM:HiChiP_CTCF_2M_R2 -p 1 -x /Users/RobertoFerrari/Downloads/bowtie_indexes//hg38 -U rawdata/sample1/HiChiP_CTCF_2M_R2.fastq.gz 2>> logs/sample1/HiChiP_CTCF_2M_R2_bowtie2.log> bowtie_results/bwt2_global/sample1/HiChiP_CTCF_2M_R2_hg38.bwt2glob.bam zsh: no such file or directory: logs/sample1/HiChiP_CTCF_2M_R2_bowtie2.log

[robeach78]

what about this: libtbb.dylib

I dont have it

(base) ➜ HiC-Pro-master /usr/bin/lib libnetcfg libnetcfg5.18 libnetcfg5.28 libtool

[nservant]

this is not the same error ... remove the log part, and be sure that paths to the data are correct

Applications/anaconda3/bin/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/sample1/HiChiP_CTCF_2M_R2_hg38.bwt2glob.unmap.fastq --rg-id BMG --rg SM:HiChiP_CTCF_2M_R2 -p 1 -x /Users/RobertoFerrari/Downloads/bowtie_indexes//hg38 -U rawdata/sample1/HiChiP_CTCF_2M_R2.fastq.gz

[nservant]

How to do you generate your conda ? did you use the environment.yml file ?

[robeach78]

yes I used the enviromental.yml

this is the error now:

/Applications/anaconda3/bin/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/sample1/HiChiP_CTCF_2M_R2_hg38.bwt2glob.unmap.fastq --rg-id BMG --rg SM:HiChiP_CTCF_2M_R2 -p 1 -x /Users/RobertoFerrari/Downloads/bowtie_indexes//hg38 -U rawdata/sample1/HiChiP_CTCF_2M_R2.fastq.gz dyld: Library not loaded: @rpath/libtbb.dylib Referenced from: /Applications/anaconda3/bin/bowtie2-align-s Reason: image not found (ERR): Description of arguments failed!

[nservant]

are you on mac OS ?

[robeach78]

yes mac OS Catalina 10.15.7

[nservant]

I think that's a pure system issue. Difficult to help you. here is the first link I found on google ... you should investigate this issue https://stackoverflow.com/questions/17703510/dyld-library-not-loaded-reason-image-not-found

[robeach78]

Thanks I ll look into it...

[robeach78]

I think that's a pure system issue. Difficult to help you. here is the first link I found on google ... you should investigate this issue https://stackoverflow.com/questions/17703510/dyld-library-not-loaded-reason-image-not-found

if it happens to someone the solution seemed to be "brew install bowtie2"

[robeach78]

another error

Thu Mar 4 21:18:22 CET 2021 Generate binned matrix files ... hg38.genome not found. Exit make: *** [/usr/local/bin/HiC-Pro_3.0.0/bin/../scripts//Makefile:174: build_raw_maps] Error 255

[nservant]

please provide the chromosome size file for hg18

GENOME_SIZE = hg38.genome

[robeach78]

I did:

Annotation files

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

REFERENCE_GENOME = hg38 GENOME_SIZE = hg38.genome

####################################################################### Allele specific analysis

see above.

the file is in the same folder

[nservant]

by default, HiC-Pro is looking for annotation in the annotation folder (in the installation repo). Otherwise, you can provide the full path to the file

[robeach78]

got it... thanks a lot!

Great support (live) ;)