Open yuyuyu-fy opened 2 years ago
Hello @yuyuyu-fy,
Can you let me know what files you use as input and their format (copy-paste the output from head <file>
), especially the format of the abundance file?
Thank you!
command is
abundance file
contigs file
gfa file
Hello @yuyuyu-fy,
I'm extremely sorry for the late reply. Can you share the files you are using so I can run a test?
Thank you!
Hello @Vini2,
I'm also trying to run MetaCoAG for a megahit assembly and getting the error described above.
This is the code I used to produce the input files
megahit_core contig2fastg k-value path/to/contigs > path/to/fastg_out
(also used megahit_toolkit)
gfastats path/to/fastg_out -o gfa > path/to/gfa_out
coverm contig -1 path/to/read1 -2 path/to/read2 -r path/to/contigs -o path/to/abundance -t 8 && sed -i '1d' path/to/abundance
MetaCoAG code:
metacoag --assembler megahit --graph path/to/gfa_out --contigs path/to/contigs --abundance path/to/abundance --output path/to/binning/
I've tried to modify the contigs.fa file:
I've also tried to run it with the data you used in your paper (accession numbers ERR970400, ERR970477) Always got the same error..
I suspect the problem is that there is no connection between the contigs header and the fastg header. Could you help me, I don't know what else to try?
Thanks!
Hi @josefawelling,
Thanks for your interest in MetaCoAG.
Can you show me the first few lines of your --graph
file and --contigs
file?
Also, can you try running metacoag with the --assembler
parameter as megahitc
and see if it works.
Let me know what happens!
Hi @Vini2,
thanks for the quick reply!
Changing to --assembler megahitc
leads to the same key error.
Here are the first few lines of the contig & graph files.
Hello! Sorry to bother you again. I ran several experiments with metacoag. There is no problem with running in spades mode, but this error is always reported when running several samples in megahit mode. I suspect it is the problem of name and ID. how can we solve it?