Majority of MAGs removed

[jronwalker]

Hello,

I recently tried to run the metator pipeline command with scaffolds from metaSPADES and the reads from HiC sequencing. The command used was
metator pipeline --assembly all_MAH_C_scaffolds.fasta --forward 0_1367337_S8_R1_001.fastq.gz --reverse 0_1367337_S8_R2_001.fastq.gz --algorithm louvain --aligner bowtie2 --aligner-mode normal --cluster-matrix False --depth None --edge 0 --enzyme None --force False --iterations 100 --rec-iter 10 --junctions NNNNN --no-clean-up False --normalization empirical_hit --outdir metator_mah_c --overlap 80 --prefix None --rec-overlap 90 --min-quality 30 --res-param 1.0 --size 500000 --start fastq --scaffold False --threads 16 --tmpdir ./tmp

I got the following warning through out the output stream BiopythonDeprecationWarning: GC is deprecated; please use gc_fraction instead. warnings.warn
My main concern is we went from 83,147 overlapping MAGs down to 3 MAGs in the next step and these were the final output MAGs. These were all classified as Others Bins and not as HQ, MQ or LQ. There was also a warning and error at the end of the log file that said:

`INFO :: HQ MAGs: 0 Total Size: 0
INFO :: MQ MAGs: 0 Total Size: 0
INFO :: LQ MAGs: 0 Total Size: 0
INFO :: Contaminated potential MAGs: 0 Total Size: 0
INFO :: Others bins: 3 Total Size: 4936961
WARNING :: No pairs alignment files found in metator_mah_c, no heatmap will be generated.
/nethome/jrw14219/miniforge3/envs/metator/lib/python3.10/site-packages/metator/figures.py:918: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
contigs_data["size_weight"] = (contigs_data["Size"] / min_size).apply(int)
INFO ::

INFO :: ## date: 2024-11-19 23:32:28`

I am using MetaTOR: v1.3.2. We have about 3M scaffolds and our HiC reads have 148M reads. Any information you could provide on what may going on or how we can optimize parameters would be greatly appreciated.

Thank you!