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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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There is no contig.fasta in my output dir #1306

Closed SoSongzhi closed 4 months ago

SoSongzhi commented 4 months ago

Description of bug

image

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

spades.log

params.txt

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

asl commented 4 months ago

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