SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Threshold quality score to determine the quality read of ILLUMINA reads problem edge Illumina/Solexa 35 11-02-2015 10:31 AM
SPAdes: erroneous kmer threshold bio_informatics Bioinformatics 9 05-17-2015 05:03 PM
how to set SNP QUAL threshold volavii Bioinformatics 0 07-08-2013 06:47 AM
how to determine the RPM threshold for MeDIP zchou Bioinformatics 0 12-01-2011 01:52 AM

Reply
 
Thread Tools
Old 03-01-2020, 10:53 PM   #1
bioramg
Member
 
Location: South Korea

Join Date: Apr 2014
Posts: 10
Default 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 spades.log file for your reference. Please find and suggest me what could be the problem and how to solve it..

Thank you.
Attached Files
File Type: txt warnings.txt (605 Bytes, 0 views)
bioramg is offline   Reply With Quote
Reply

Tags
bbmap, hybrid assembly, illumina & 454, nanopore miniion, spades

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:26 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO