search

ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
739 stars 134 forks source link

SPAdes: K21,33,55,77,99,127, didtn't generate any data in files: scaffolds.gfa and contigs.fasta #1322

Closed 02Julie2023 closed 3 months ago

02Julie2023 commented 3 months ago

Description of bug

After running the SPAdes, it doesn't generate any data in the files below: assembly_graph_after_simplification.gfa assembly_graph.fastg assembly_graph_with_scaffolds.gfa before_rr.fasta contigs.fasta Could you please take a look at it? I appreciate it.

spades.log

warnings.log stdout.12768013.pdf

params.txt

params.txt

SPAdes version

SPAdes / 3.15.5

Operating System

macOS Sonoma Version 14.4.1

Python Version

Python 3.11.1

Method of SPAdes installation

pip

No errors reported in spades.log

asl commented 3 months ago

So, the log reads:

(simplification.cpp : 495) After simplification: 
0:01:14.501 1M / 5155M INFO General
(simplification.cpp : 496) Average coverage = 0
0:01:14.501 1M / 5155M INFO General
(simplification.cpp : 497) Total length = 0
0:01:14.502 1M / 5155M INFO General
(simplification.cpp : 498) Median edge length: 0
0:01:14.502 1M / 5155M INFO General
(simplification.cpp : 499) Edges: 0
0:01:14.502 1M / 5155M INFO General
(simplification.cpp : 500) Vertices: 0
0:01:14.502 1M / 5155M WARN General

Given that you're having less than 1k reads, it does not seem to be a genome or a part of any genome, so your reads simply do not assemble at all.