Question: Issues running Masurca
0
gravatar for naro2013
3 months ago by
naro20130
naro20130 wrote:

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!

next-gen assembly • 172 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by naro20130

Please edit your question and add masurca as a tag so people looking to answer Masurca questions can find your question easily.

ADD REPLYlink written 3 months ago by RamRS20k
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