Bowtie error and stopped pipeline

[Rayko87]

Hello,

I have been running HiCpro in one sample ( I only have one sample divided in two fast (R1 and R2) and the last files produced were )and I got this error:

Wed Oct 9 10:42:51 EDT 2019 Bowtie2 alignment step2 ... Logs: logs/rawdata/mapping_step2.log Logs: logs/sample1/mapping_step2.log /mnt/data/robert/programs/HiC-Pro_2.11.1/scripts/bowtie_wrap.sh: line 87: echo: write error: No space left on device /mnt/data/robert/programs/HiC-Pro_2.11.1/scripts/bowtie_wrap.sh: line 87: echo: write error: No space left on device Exit: Error in reads alignment - Exit /mnt/data/robert/programs/HiC-Pro-2.11.1/bin/../scripts//Makefile:98: recipe for target 'bowtie_local' failed make: *** [bowtie_local] Error 1

As a result, the pipeline stopped. However, it did not stopped the 9 of October, it went on with the bowtie analysis.... The last files produced were:

New_analysis_HiCpro/results_dnd41_hicpro/bowtie_results/bwt2_local/sample1/HiChip27-DND41_R2_001_GRChg37-hg19.bwt2glob.unmap_trimmed.fastq.

The problem is I have not space in disk? Do I have to start from the beginning or I can go on from this point. The analysis took 7 days to arrive to this point (each of the two fastq.gz are 30G).

Thanks!

Robert

[nservant]

Hi Robert, I'm afraid you will need to start from the beginning ! However, do you have access to a cluster ? If so you can split your files into smaller chunks and run all chunks in parallel with '-p' option (see doc for more details) ? Best

[Rayko87]

Hello!

Repeating it, I realize that the raw data and the sample1 (I only have one sample) are doing the same alignment. Consequently, the pipeline takes the double time. Is there a way to speed this up in a configuration file when you only have one sample?

Thanks!

[nservant]

I think there is something wrong in the way you specify the input data. Could you show me how your input data are organized ? and your command line please ? Thanks

[Rayko87]

Sure.

I only run this command: HiC-Pro -i /mnt/data/fastq/DND41-HiChip -o Second_analysis_DND41_HiCpro -c config-hicpro.txt

From this pwd: /mnt/data/ANALISIS/New_analysis_HiCpro. It is inside this folder where I have the config-hicpro.txt and the GATC_hg19 (my enzyme cutting file). In this folder it is where the a subfolder called Second_analysis_DND41_HiCpro has been generated, with all the files of the analysis.

I have my fastq.gz (R1 and R2) in this directory: /mnt/robert/fastq/DND41-HiChip/sample1

My pipeline is still running (I got this so far:)

Run HiC-Pro 2.11.1

Fri Oct 11 13:41:22 EDT 2019 Bowtie2 alignment step1 ... Logs: logs/rawdata/mapping_step1.log Logs: logs/sample1/mapping_step1.log

---

Sun Oct 20 04:12:31 EDT 2019 Bowtie2 alignment step2 ... Logs: logs/rawdata/mapping_step2.log Logs: logs/sample1/mapping_step2.log

My config-hicpro.txt file is this:

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 = 11 LOGFILE = hicpro.log

JOB_NAME = JOB_MEM = JOB_WALLTIME = JOB_QUEUE = JOB_MAIL =

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

Data

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

PAIR1_EXT = _R1_001 PAIR2_EXT = _R2_001

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

Alignment options

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

MIN_MAPQ = 10

BOWTIE2_IDX_PATH =/mnt/data/robert/index_and_genome_files 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 = GRChg37-hg19 GENOME_SIZE = chrom_hg19.sizes

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

Allele specific analysis

#######################################################################AALLELE_SPECIFIC_SNP =

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

Capture Hi-C analysis

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

CAPTURE_TARGET = REPORT_CAPTURE_REPORTER = 1

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

Digestion Hi-C

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

GENOME_FRAGMENT = /mnt/data/ANALISIS/New_analysis_HiCpro/GATC_hg19 LIGATION_SITE = GATCGATC 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

Thanks for all your help

[wzhjlau2009]

@Rayko87 ，Hi I got the same error as you list, can you tell me how to solve this problem? Thanks very much!

The Best!