Hi everyone, I'm having some troubles running the following assembly script in Masurca.
DATA
PE = p1 261.98 87.34 /opt/18Bioinf/FESIZTA_1.fastq /opt/18Bioinf/FESIZTA_2.fastq PE = p2 382.98 100.45 /opt/18Bioinf/CAR-16_S2_R1_001.fastq /opt/18Bioinf/CAR-16_S2_R2_001.fastq
END
PARAMETERS
GRAPH_KMER_SIZE = auto
USE_LINKING_MATES = 0
USE_GRID=1
GRID_QUEUE=all.q
GRID_BATCH_SIZE=300000000
LHE_COVERAGE=30
LIMIT_JUMP_COVERAGE = 300
CA_PARAMETERS = cgwErrorRate=0.15
KMER_COUNT_THRESHOLD = 1
CLOSE_GAPS=1
NUM_THREADS = 16
JF_SIZE = 187300474929
SOAP_ASSEMBLY=0
END
The problem here is that I ran a few times the assembly and it never displays anything on the terminal (about errors or parameters I need to change, it only appears "Processing pe library reads" along the run) and when it finishes I only got the files: assemble.sh, environment.sh, config_file, meanAndStdevByPrefix, p1.renamed.fastq, p2.renamed.fastq and pe_data.tmp. Also it does not create the log file and the. About the final result file, I have the doubt about what "the final assembly scaffolds file is under CA/ or CA.mr...../ "
I hope you can help me, I'm doing this against time. Thnk you!
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