Several errors: finished abnormally, OS return value: 21 None, Too many erroneous kmers, the estimates might be unreliable, Invalid kmer coverage histogram, make sure that the coverage is indeed uniform and Failed to determine erroneous kmer threshold. Threshold set to: 3

ablab / spades

SPAdes Genome Assembler

http://ablab.github.io/spades/

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Several errors: finished abnormally, OS return value: 21 None, Too many erroneous kmers, the estimates might be unreliable, Invalid kmer coverage histogram, make sure that the coverage is indeed uniform and Failed to determine erroneous kmer threshold. Threshold set to: 3 #1276

Closed Wyclif3 closed 2 months ago

Wyclif3 commented 2 months ago

Description of bug

Spades is failing to assemble some of my reads. I have tried to change the Kmer values and the problem still persists with several abnormalities.

spades.log

params.txt

spades_redo.log

SPAdes version

3.15.0

Operating System

linux

Python Version

3.8.4

Method of SPAdes installation

binaries

No errors reported in spades.log

[X] Yes

asl commented 2 months ago

You are only having 40 reads. This does not look like as something as a genome or some well-covered / well-formed part of it.

Wyclif3 commented 2 months ago

This means some of the data are of low quality ? I already performed data cleaning in trimmomatic before assembling genes in hybpiper. What is the best solution for my problem at this point?