Bowtie stopped when mapping the last set of files

[xianqiang wang]

Hi,

I'm running the HiC-Pro with my own data, the HiC data contains 8 pairs fastq files, but it stopped when mapping the last pair of fastq files through bowtie.

This is my file structure:

├── annotation
│   ├── Arabidopsis.sizes
│   ├── Arabidopsis_thaliana.TAIR10.dna.toplevel.fa
│   └── DpnI_HinfI_Arabidopsis.bed
├── config
│   └── config-hicpro.txt
├── index
│   ├── Arabidopsis.1.bt2
│   ├── Arabidopsis.2.bt2
│   ├── Arabidopsis.3.bt2
│   ├── Arabidopsis.4.bt2
│   ├── Arabidopsis.rev.1.bt2
│   └── Arabidopsis.rev.2.bt2
└── reads
    └── FRI-NV_S2
        ├── FRI-NV_S2_L001_R1.fastq.gz
        ├── FRI-NV_S2_L001_R2.fastq.gz
        ├── FRI-NV_S2_L002_R1.fastq.gz
        ├── FRI-NV_S2_L002_R2.fastq.gz
        ├── FRI-NV_S2_L003_R1.fastq.gz
        ├── FRI-NV_S2_L003_R2.fastq.gz
        ├── FRI-NV_S2_L004_R1.fastq.gz
        ├── FRI-NV_S2_L004_R2.fastq.gz
        ├── FRI-NV_S2_L005_R1.fastq.gz
        ├── FRI-NV_S2_L005_R2.fastq.gz
        ├── FRI-NV_S2_L006_R1.fastq.gz
        ├── FRI-NV_S2_L006_R2.fastq.gz
        ├── FRI-NV_S2_L007_R1.fastq.gz
        ├── FRI-NV_S2_L007_R2.fastq.gz
        ├── FRI-NV_S2_L008_R1.fastq.gz
        └── FRI-NV_S2_L008_R2.fastq.gz

This 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 = 8
SORT_RAM = 1000M
LOGFILE = hicpro.log

JOB_NAME =
JOB_MEM = 8gb
JOB_WALLTIME =
JOB_QUEUE =
JOB_MAIL =

#########################################################################
## Data
#########################################################################

PAIR1_EXT = _R1
PAIR2_EXT = _R2

#######################################################################
## Alignment options
#######################################################################

MIN_MAPQ = 10

BOWTIE2_IDX_PATH = /home/xianqiang/Documents/project/HiC/index/
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 = Arabidopsis
GENOME_SIZE = /home/xianqiang/Documents/project/HiC/annotation/Arabidopsis.sizes

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

ALLELE_SPECIFIC_SNP =

#######################################################################
## Capture Hi-C analysis
#######################################################################

CAPTURE_TARGET =
REPORT_CAPTURE_REPORTER = 1

#######################################################################
## Digestion Hi-C
#######################################################################

GENOME_FRAGMENT = /home/xianqiang/Documents/project/HiC/annotation/DpnI_HinfI_Arabidopsis.bed
LIGATION_SITE = GATCGATC,GATCGANT,GANTGATC,GANTGANT
MIN_FRAG_SIZE = 100
MAX_FRAG_SIZE = 100000
MIN_INSERT_SIZE = 100
MAX_INSERT_SIZE = 1000

#######################################################################
## 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 = 10000 50000 100000 500000 1000000
MATRIX_FORMAT = upper

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

The below is files of results

.
├── bowtie_results
│   └── bwt2_global
│       └── FRI-NV_S2
│           ├── FRI-NV_S2_L001_R1_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L001_R1_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L001_R2_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L001_R2_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L002_R1_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L002_R1_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L002_R2_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L002_R2_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L003_R1_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L003_R1_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L003_R2_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L003_R2_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L004_R1_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L004_R1_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L004_R2_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L004_R2_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L005_R1_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L005_R1_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L005_R2_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L005_R2_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L006_R1_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L006_R1_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L006_R2_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L006_R2_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L007_R1_Arabidopsis.bwt2glob.bam
│           ├── FRI-NV_S2_L007_R1_Arabidopsis.bwt2glob.unmap.fastq
│           ├── FRI-NV_S2_L007_R2_Arabidopsis.bwt2glob.bam
│           └── FRI-NV_S2_L007_R2_Arabidopsis.bwt2glob.unmap.fastq
├── config-hicpro.txt
├── logs
│   └── FRI-NV_S2
│       ├── FRI-NV_S2_L001_R1_bowtie2.log
│       ├── FRI-NV_S2_L001_R2_bowtie2.log
│       ├── FRI-NV_S2_L002_R1_bowtie2.log
│       ├── FRI-NV_S2_L002_R2_bowtie2.log
│       ├── FRI-NV_S2_L003_R1_bowtie2.log
│       ├── FRI-NV_S2_L003_R2_bowtie2.log
│       ├── FRI-NV_S2_L004_R1_bowtie2.log
│       ├── FRI-NV_S2_L004_R2_bowtie2.log
│       ├── FRI-NV_S2_L005_R1_bowtie2.log
│       ├── FRI-NV_S2_L005_R2_bowtie2.log
│       ├── FRI-NV_S2_L006_R1_bowtie2.log
│       ├── FRI-NV_S2_L006_R2_bowtie2.log
│       ├── FRI-NV_S2_L007_R1_bowtie2.log
│       ├── FRI-NV_S2_L007_R2_bowtie2.log
│       └── mapping_step1.log
├── rawdata -> /home/xianqiang/Documents/project/HiC/reads/
└── tmp

I tried two times, but it all failed when mapping the 8th pair of fastq files, how could I solve that?

Thanks for your support!

Best regards, 

Xianqiang 

[nservant]

Hi

Do you have any specific message ? could it be a time out issue on your server ?

N