ablab
What is the rationale of jump in contigs.paths?
Description of bug
Hi there, I have a question:
metaSPAdes has output 'contigs.paths' which contains the path of segments connected either by links (denoted by a comma between segments) or by jumps (denoted by a semicolon between segments).
My understanding is that jump is something you use to put multiple contigs on a scaffold and the contigs connect to each other on the scaffold via jump.
So I expect jumps in 'scaffolds.paths', but why are there jumps in 'contigs.paths' as well, which should represent solely contigs?
spades.log
params.txt
SPAdes version
SPAdes v4.0.0
Operating System
Red Hat Enterprise Linux 9.0
Python Version
Python 3.13.0
Method of SPAdes installation
conda
No errors reported in spades.log
- [x] Yes
You're right, this seems to be some kind of issue. Is it possible for you to share a reproducer with us?
Hi there, thank you for the response. Can you specify what do you want me to share here?
The parameters and settings are given above in the params.txt. The jump presence in contigs.paths is very prevalent from my experience working with multiple read files.
One of the read files can be downloaded here: wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR154/000/ERR1543540/ERR1543540_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR154/000/ERR1543540/ERR1543540_2.fastq.gz
Do you think this is an issue where the contigs.fasta erroneously included these jump-containing contigs (and it should be included in the scaffold.fasta instead)? Or are there supposed to be no jump to begin with between those segments?