I am trying to run my first hybrid assembly with MaSuRCA 3.2.7 with the following config file:
DATA PE= pe 350 50 /fullpath/R1.fastq.gz /fullpath/R2.fastq.gz #JUMP= sh 3600 200 /FULL_PATH/short_1.fastq /FULL_PATH/short_2.fastq #pacbio reads must be in a single fasta file! make sure you provide absolute path PACBIO=/fullpath/pacbio.fastq.gz #OTHER=/FULL_PATH/file.frg END PARAMETERS #set this to 1 if your Illumina jumping library reads are shorter than 100bp EXTEND_JUMP_READS=0 #this is k-mer size for deBruijn graph values between 25 and 127 are supported, auto will compute the optimal size based on the read data and GC content GRAPH_KMER_SIZE = auto #set this to 1 for all Illumina-only assemblies #set this to 1 if you have less than 20x long reads (454, Sanger, Pacbio) and less than 50x CLONE coverage by Illumina, Sanger or 454 mate pairs #otherwise keep at 0 USE_LINKING_MATES = 0 #specifies whether to run mega-reads correction on the grid USE_GRID=0 #specifies queue to use when running on the grid MANDATORY GRID_QUEUE=all.q #batch size in the amount of long read sequence for each batch on the grid GRID_BATCH_SIZE=300000000 #coverage by the longest Long reads to use LHE_COVERAGE=30 #this parameter is useful if you have too many Illumina jumping library mates. Typically set it to 60 for bacteria and 300 for the other organisms LIMIT_JUMP_COVERAGE = 300 #these are the additional parameters to Celera Assembler. do not worry about performance, number or processors or batch sizes -- these are computed automatically. #set cgwErrorRate=0.25 for bacteria and 0.1<=cgwErrorRate<=0.15 for other organisms. CA_PARAMETERS = cgwErrorRate=0.15 #minimum count k-mers used in error correction 1 means all k-mers are used. one can increase to 2 if Illumina coverage >100 KMER_COUNT_THRESHOLD = 1 #whether to attempt to close gaps in scaffolds with Illumina data CLOSE_GAPS=1 #auto-detected number of cpus to use NUM_THREADS = 4 #this is mandatory jellyfish hash size -- a safe value is estimated_genome_size*estimated_coverage JF_SIZE = 200000000 #set this to 1 to use SOAPdenovo contigging/scaffolding module. Assembly will be worse but will run faster. Useful for very large (>5Gbp) genomes from Illumina-only data SOAP_ASSEMBLY=0 END
However after creating and running the assemble script I get this error:
Error correction of PE reads failed. Check pe.cor.log.
I cannot find the pe.cor.log file. Please could you help me fix this issue.