question of megahit

[yuyuyu-fy]

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?

[Vini2]

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!

[yuyuyu-fy]

command is

abundance file

contigs file

gfa file

[Vini2]

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!

[josefawelling]

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:

1. rename fasta header & remove the k-value (see above 'k141_' )
2. sort fasta file by renamed ID

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!

[Vini2]

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!

[josefawelling]

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.

[yazhinia]

Hi @Vini2,
I am trying to bin megahit assembled contigs. Using the megahit_toolkit and fastg2gfa to convert fa to gfa results in the loss of contig ID information in the final 'gfa' file. Have you found any solution to this problem?