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alekseyzimin / masurca

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no genome.ctg.fasta #22

Open hzz0024 opened 6 years ago

hzz0024 commented 6 years ago

We used MASURCA 3.2.6 for genome assembly but found no fasta file for contig sequences at the end. Only final.genome.scf.fasta appeared in the CA folder. Is this normal? Below is the content from the log file:

Processing pe library reads Average PE read length 126 Using kmer size of 83 for the graph cat: write error: Broken pipe MIN_Q_CHAR: 33 Creating mer database for Quorum Error correct PE. Estimating genome size. Estimated genome size: 697935949 Creating k-unitigs with k=83 Computing super reads from PE Celera Assembler ovlMerThreshold=75 Overlap/unitig success recomputing A-stat for super-reads recomputing A-stat for super-reads Unitig consensus success CA success No gap closing possible. Assembly complete, final scaffold sequences are in CA/final.genome.scf.fasta All done

Thanks

hzz0024 commented 6 years ago

FYI: we only used Illumina PE reads for draft genome assembly. The mean and stdev were set as 500 and 100, respectively. Other parameters were set as default. Does anybody have a clue?

alekseyzimin commented 6 years ago

Contig sequences and other outputs are under CA/9-terminator