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  • bioramg
    Member
    • Apr 2014
    • 12

    SPADES: Failed to determine erroneous kmer threshold. Threshold set to: 22

    Hi,
    Thank you for developing SPAdes for hybrid assembly.

    I tried to assemble Illumina pair-end with Oxford Nanopore Sequence for plant mitochondrial genome assembly.

    Before carried out, I used BBMAP to trim adapters and normalize Illumina data. I have used the commands for trim adapters:

    bbmap$ ./bbduk.sh -Xmx1g in=read1.fastq in2=read2.fastq out=trim_read1.fastq out2=trim_read2.fastq ktrim=r k=23 mink=11 hdist=1 ref=resources/adapters.fa tbo tpe

    for normalize:
    $./bbnorm.sh in=trim_read1.fastq in2=trim_read2.fastq out=norm_read1.fastq out2=norm_rread2.fastq target=100 min=5

    Then, I used these Illumina pair-end reads with Oxford nanopore and the commands as follows:

    $ ./spades.py -k 99 --pe1-1 norm_read1.fastq --pe1-2 norm_read2.fastq --nanopore nano_read.fastq --careful --cov-cutoff 90 -o hybrid_assembly -m 188.

    When I run using this command, I have got an error message as:
    ======= SPAdes pipeline finished WITH WARNINGS!

    === Error correction and assembling warnings:
    * 8:48:41.078 34G / 56G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable
    * 8:48:41.472 34G / 56G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 22
    * 8:48:41.477 34G / 56G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 22

    I am herewith enclosing the spades file for your reference. Please find and suggest me what could be the problem and how to solve it...[](url)
    Attached Files

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