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  • Hedi86
    Member
    • Oct 2017
    • 24
    #1

    errors at the beginning of hybrid assembly using MaSuRCA-4.0.3

    Hi

    im trying to make hybrid assembly for Ecoli using MiSeq and Nanopore data in Masurca. currently i m getting two errors marked in Bold bellow. my MinION fastq files should be OK, no idea why im getting such errors.

    any helps would be appreciate.

    /Downloads/MaSuRCA-4.0.3/bin/masurca -t 32 -i MiSeq_R1.fastq MiSeq_R2.fastq -r MinION.fastq

    Verifying PATHS...
    jellyfish OK
    runCA OK
    createSuperReadsForDirectory.perl OK
    creating script file for the actions...done.
    execute assemble.sh to run assembly
    [fr. 04. juni 15:42:56 +0200 2021] Processing pe library reads
    [fr. 04. juni 15:42:56 +0200 2021] Average PE read length 250
    [fr. 04. juni 15:42:56 +0200 2021] Using kmer size of 127 for the graph
    [fr. 04. juni 15:42:56 +0200 2021] MIN_Q_CHAR: 33
    [fr. 04. juni 15:42:56 +0200 2021] Estimated genome size: 5058150
    [fr. 04. juni 15:42:56 +0200 2021] Computing super reads from PE
    [fr. 04. juni 15:42:56 +0200 2021] Using CABOG from /Downloads/MaSuRCA-4.0.3/bin/../CA8/Linux-amd64/bin
    [fr. 04. juni 15:42:56 +0200 2021] Running mega-reads correction/assembly
    [fr. 04. juni 15:42:56 +0200 2021] Using mer size 17 for mapping, B=15, d=0.02
    [fr. 04. juni 15:42:56 +0200 2021] Estimated Genome Size 5058150
    [fr. 04. juni 15:42:56 +0200 2021] Estimated Ploidy 1
    [fr. 04. juni 15:42:56 +0200 2021] Using 32 threads
    [fr. 04. juni 15:42:56 +0200 2021] Output prefix mr.41.17.15.0.02
    [fr. 04. juni 15:42:56 +0200 2021] Pre-correction and initial filtering of the long reads
    [fr. 04. juni 15:42:57 +0200 2021] Failed to pre-correct MinION.fastq file, please check your data!
    [fr. 04. juni 15:42:57 +0200 2021] mega-reads exited before assembly
    Tags: hybrid assembly, masurca, minion, miseq, nanopore
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