There is no contig.fasta in my output dir
SoSongzhi opened this issue · 1 comments
SoSongzhi commented
Description of bug
![image](https://private-user-images.githubusercontent.com/74604653/332716927-20bfddbd-fbd4-4e44-8c22-5cbe282e292c.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.qAb-9gXtVD_4QxgwEQ--UyXJx7JsiUXbjK5FD1I6YQU)
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