Max bin don't find enough marker genes.

[SilasK]

I had several times the problem that maxbin gave me the following error.

MaxBin 2.2.1
Input contig: F35/F35_contigs.fasta
Located abundance file [F35/genomic_bins/F35_contig_coverage.tsv]
out header: F35/genomic_bins/F35
Min contig length: 200
Thread: 6
Probability threshold: 0.9
Max iteration: 50
Searching against 107 marker genes to find starting seed contigs for [F35/F35_contigs.fasta]...
Try harder to dig out marker genes from contigs.
Marker gene search reveals that the dataset cannot be binned (the medium of marker gene number <= 1). Program stop.

But my contigs statistics don't look so bad. I don't know what's the problem.

n_scaffolds | scaf_bp    | scaf_N50 | scaf_L50 | scaf_N90 | scaf_L90 | scaf_max |
12470         | 65564177 | 1130       | 13095       | 7423        | 1725       | 165795     | 

and the cov file looks like this:

F35_0   18.9348
F35_1   15.5894
F35_2   18.8915
F35_3   20.1290
F35_4   28.7693
F35_5   33.6804
F35_6   24.2962
F35_7   19.3721
F35_8   20.3123
F35_9   17.1395

[brwnj]

I'm running into the same thing. We could likely add support for alternative binning codes as you previously suggested, like CONCOCT, GroopM, and/or MetaBAT.

[vindarbot]

I had the same problem, after deletes files from a previous analysis (same output: rm sample_0/maxbin/MaxBin.out*), run_Maxbin.pl finally worked properly.

[CMagnoBR]

Hi everyone! Sorry for reopen this issue.
I had the same problem here, when using Atlas version: 2.14.3 Snakemake 7.18.2, with SE reads. Its seems some problem in the maxbin binning step. Below is the maxbin.log:

MaxBin 2.2.7
Input contig: SRR19257246.trim.woutplant/SRR19257246.trim.woutplant_contigs.fasta
Located abundance file [SRR19257246.trim.woutplant/binning/coverage/SRR19257246.trim.woutplant_coverage.txt]
out header: SRR19257246.trim.woutplant/binning/maxbin/intermediate_files/SRR19257246.trim.woutplant
Min contig length: 1000
Thread: 8
Probability threshold: 0.9
Max iteration: 50
Searching against 107 marker genes to find starting seed contigs for [SRR19257246.trim.woutplant/SRR19257246.trim.woutplant_contigs.fasta]...
Running FragGeneScan....
Running HMMER hmmsearch....
Try harder to dig out marker genes from contigs.
Marker gene search reveals that the dataset cannot be binned (the medium of marker gene number <= 1). Program stop.

Please, help me!

[SilasK]

You have the folowing options:

1. Use a other final_binner e.g. vamb or metabat.
2. remove the sample from the sample.tsv

• I should add the option to exclude a sample only for the binning but not for quantification

[mladen5000]

Still having this issue, just a thought - would it be possible to touch a file upon completion of maxbin (or Semibin, vamb, etc).

You have the folowing options:

1. Use a other `final_binner` e.g. vamb or metabat.

2. remove the sample from the sample.tsv


* [ ]  I should add the option to exclude a sample only for the binning but not for quantification

[SilasK]

Lets discuss on #651

[LLansing]

I've had the exact log for maxbin as CMagnoBR for 4/14 of my samples.
I understand that choosing a different binner is an option, but @SilasK could you please provide some context as to what the output means and what this means about my samples?

[SilasK]

As I understand it. maxbin estimates how many genomes can be found in a sample to set binning parameters.
If it doesn't find marker genes it says it cannot bin. This probably means that your sample is too shallow or not well assembled.
Other binners might recover bins, but likely not too many hq bins anyway.

Unfortunately, there is no easy way in atlas to ignore such a sample for now. We are working on it #651 .

But for now best options are to drop very bad samples and or choose another binner, e.g. vamb.