Hi,dear
when I run Correct process of Mecat2, at the stage of mecat2pw it aborted with one error.my config file as follows:
PROJECT=ma
RAWREADS=ma.subreads.fastq
GENOME_SIZE=530000000
THREADS=100
MIN_READ_LENGTH=2000
CNS_OVLP_OPTIONS="-j 1 -d ma.subreads.fastq -t 30 -o ma -n 50 -k 18"
CNS_OPTIONS="-i 1 -t 32 -p 100000 -r 0.6 -a 1000 -c 4 -l 2000"
TRIM_OVLP_OPTIONS="-B"
ASM_OVLP_OPTIONS="-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 0 -a 400"
FSA_OL_FILTER_OPTIONS="max_overhang=-1 --min_coverage=-1 --max_coverage=-1 --max_diff_coverage=-1 --overlap_file_type=m4 --genome_size=530000000 output_directory=mecat_assembly --thread_size=32"
FSA_ASSEMBLE_OPTIONS="--min_length=2500 --min_identity=90 --min_aligned_length=2500 --min_contig_length=10000 --read_file=ma.subreads.fastq --overlap_file_type=m4 --output_directory=mecat_assembly --select_branch=best"
USE_GRID=true
CLEANUP=0
CNS_OUTPUT_COVERAGE=30
GRID_NODE=8
the job submission system is sge, the error information is
/scripts/cns_pw.sh: line 11: 27508 Aborted (core dumped)
2019-09-25 17:54:30 [Error] Failed to run script, 134,mecat_assembly/ma/scripts/cns_pw.sh
Could help me resolve it ? I cannot figure out.Thanks very much!
Hi,dear
when I run Correct process of Mecat2, at the stage of mecat2pw it aborted with one error.my config file as follows:
PROJECT=ma
RAWREADS=ma.subreads.fastq
GENOME_SIZE=530000000
THREADS=100
MIN_READ_LENGTH=2000
CNS_OVLP_OPTIONS="-j 1 -d ma.subreads.fastq -t 30 -o ma -n 50 -k 18"
CNS_OPTIONS="-i 1 -t 32 -p 100000 -r 0.6 -a 1000 -c 4 -l 2000"
TRIM_OVLP_OPTIONS="-B"
ASM_OVLP_OPTIONS="-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 0 -a 400"
FSA_OL_FILTER_OPTIONS="max_overhang=-1 --min_coverage=-1 --max_coverage=-1 --max_diff_coverage=-1 --overlap_file_type=m4 --genome_size=530000000 output_directory=mecat_assembly --thread_size=32"
FSA_ASSEMBLE_OPTIONS="--min_length=2500 --min_identity=90 --min_aligned_length=2500 --min_contig_length=10000 --read_file=ma.subreads.fastq --overlap_file_type=m4 --output_directory=mecat_assembly --select_branch=best"
USE_GRID=true
CLEANUP=0
CNS_OUTPUT_COVERAGE=30
GRID_NODE=8
the job submission system is sge, the error information is
/scripts/cns_pw.sh: line 11: 27508 Aborted (core dumped)
2019-09-25 17:54:30 [Error] Failed to run script, 134,mecat_assembly/ma/scripts/cns_pw.sh
Could help me resolve it ? I cannot figure out.Thanks very much!