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 spades.log file for your reference. Please find and suggest me what could be the problem and how to solve it..
Thank you.
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 spades.log file for your reference. Please find and suggest me what could be the problem and how to solve it..
Thank you.