There is no contig.fasta in my output dir
SoSongzhi opened this issue · 1 comments
SoSongzhi commented
Description of bug
even though i got several files after i use spades to assemble simulated reads, but i can not found contig fasta. Do you know why it happened? thanks.
spades.log
params.txt
SPAdes version
3.16.0-dev
Operating System
macOS Ventura Version 13.6
Python Version
Python 3.8.4
Method of SPAdes installation
manual from github
No errors reported in spades.log
- Yes
asl commented
The log clearly reads:
=== ERRORs:
* 0:00:01.264 1M / 18M ERROR General (kmer_coverage_model.cpp : 188) Invalid kmer coverage histogram, make sure that the coverage is indeed uniform
* system call for: "['/Users/zhisong/Desktop/spades/bin/spades-core', '/Users/zhisong/Desktop/spades/testfasta1/K127/configs/config.info', '/Users/zhisong/Desktop/spades/testfasta1/K127/configs/isolate_mode.info']" finished abnormally, OS return value: 255
Given that you are having only 1000 reads and maximum read length is 6899 bp with average of 1728.57 bp, this does not look like a valid input data