Error in rule run_checkm2: No DIAMOND annotation was generated

[bioinfogini]

Hello there,
I was running atlas binning and got to a good 94% of the job done when, while running CheckM2, I got stuck.
Print out is the following:

[] INFO: Running CheckM2 version 1.0.2
[] INFO: Running quality prediction workflow with 70 threads.
[] INFO: Calling genes in 1 bins with 70 threads:
Finished processing 1 of 1 (100.00%) bins.
[] INFO: Calculating metadata for 1 bins with 70 threads:
Finished processing 1 of 1 (100.00%) bin metadata.
[] INFO: Annotating input genomes with DIAMOND using 70 threads
[] INFO: Processing DIAMOND output
[] ERROR: No DIAMOND annotation was generated.

As far as I can see, it performed this twice, both on the same sample, and got stuck.

Hope anyone can help or to update here with solution I could find.

UPDATE1: I checked my samples, and realised that the one generating the error was the only one presenting 1 fasta file alone in the /binning/vamb/bins folder. As it would make sense that that only bin is as well low quality and diamond cannot classify it, I (made a copy somewhere else and) removed the sample. Tried then to rerun the analysis. Will update.

Update2: Analysis got stuck again because marvellous Atlas was able to regenerate out-of-dont-know-where the "removed" sample. Pretty smart, but creating me an issue in this case. Will try to remove the sample from samples.tsv file, let's see if I can trick Atlas this way.
NOTE: Atlas get stuck even though I tried to add the --keep-going flag. It is about 96% done, 299 of 311 steps.

@SilasK if anytime you have a moment to jump in would be great! It's starting to be a pretty fun adventure.

[bioinfogini]

It worked.

So, to be precise, I removed my sample from samples.tsv file and I also moved the following files somewhere else (just in case I was wrong):

Sample/
├── Assembly
│   └── fasta
│   └── .fasta
├── Intermediate
│   ├── cobinning
│   │   ├── All
│   │   │   ├── bams
│   │   │   │   └── .sorted.bam
│   │   │   └── vamb_output
│   │   │   └── bins
│   │   └── filtered_contigs
│   │   └── .fasta.gz
│   └── qc
│   └── decontamination
│   └──
│   ├── PhiX_R1.fastq.gz
│   ├── PhiX_R2.fastq.gz
│   ├── Sscrofa_R1.fastq.gz
│   └── Sscrofa_R2.fastq.gz
├── QC
│   └── reads
│   ├── _R1.fastq.gz
│   └── _R2.fastq.gz
└──
├── annotation
│   └── predicted_genes
│   ├── .faa
│   ├── .fna
│   ├── .gff
│   └── .tsv
├── assembly
│   ├── assembly_graph_after_simplification.gfa
│   ├── assembly_graph.fastg
│   ├── assembly_graph_with_scaffolds.gfa
│   ├── before_rr.fasta
│   ├── contigs.fasta
│   ├── contigs.paths
│   ├── contig_stats
│   │   ├── final_contig_stats.txt
│   │   ├── postfilter_coverage_binned.txt
│   │   ├── postfilter_coverage_histogram.txt
│   │   └── postfilter_coverage_stats.txt
│   ├── dataset.info
│   ├── first_pe_contigs.fasta
│   ├── input_dataset.yaml
│   ├── K21
│   │   ├── configs
│   │   │   ├── careful_mda_mode.info
│   │   │   ├── careful_mode.info
│   │   │   ├── config.info
│   │   │   ├── construction.info
│   │   │   ├── detail_info_printer.info
│   │   │   ├── distance_estimation.info
│   │   │   ├── hmm_mode.info
│   │   │   ├── isolate_mode.info
│   │   │   ├── large_genome_mode.info
│   │   │   ├── mda_mode.info
│   │   │   ├── meta_mode.info
│   │   │   ├── metaplasmid_mode.info
│   │   │   ├── metaviral_mode.info
│   │   │   ├── pe_params.info
│   │   │   ├── plasmid_mode.info
│   │   │   ├── rna_mode.info
│   │   │   ├── rnaviral_mode.info
│   │   │   ├── sewage_mode.info
│   │   │   ├── simplification.info
│   │   │   └── toy.info
│   │   ├── final.lib_data
│   │   └── simplified_contigs
│   │   ├── contigs_info
│   │   ├── contigs.off
│   │   └── contigs.seq
│   ├── K33
│   │   ├── configs
│   │   │   ├── careful_mda_mode.info
│   │   │   ├── careful_mode.info
│   │   │   ├── config.info
│   │   │   ├── construction.info
│   │   │   ├── detail_info_printer.info
│   │   │   ├── distance_estimation.info
│   │   │   ├── hmm_mode.info
│   │   │   ├── isolate_mode.info
│   │   │   ├── large_genome_mode.info
│   │   │   ├── mda_mode.info
│   │   │   ├── meta_mode.info
│   │   │   ├── metaplasmid_mode.info
│   │   │   ├── metaviral_mode.info
│   │   │   ├── pe_params.info
│   │   │   ├── plasmid_mode.info
│   │   │   ├── rna_mode.info
│   │   │   ├── rnaviral_mode.info
│   │   │   ├── sewage_mode.info
│   │   │   ├── simplification.info
│   │   │   └── toy.info
│   │   ├── final.lib_data
│   │   └── simplified_contigs
│   │   ├── contigs_info
│   │   ├── contigs.off
│   │   └── contigs.seq
│   ├── K55
│   │   ├── assembly_graph_after_simplification.gfa
│   │   ├── assembly_graph.fastg
│   │   ├── assembly_graph_with_scaffolds.gfa
│   │   ├── before_rr.fasta
│   │   ├── configs
│   │   │   ├── careful_mda_mode.info
│   │   │   ├── careful_mode.info
│   │   │   ├── config.info
│   │   │   ├── construction.info
│   │   │   ├── detail_info_printer.info
│   │   │   ├── distance_estimation.info
│   │   │   ├── hmm_mode.info
│   │   │   ├── isolate_mode.info
│   │   │   ├── large_genome_mode.info
│   │   │   ├── mda_mode.info
│   │   │   ├── meta_mode.info
│   │   │   ├── metaplasmid_mode.info
│   │   │   ├── metaviral_mode.info
│   │   │   ├── pe_params.info
│   │   │   ├── plasmid_mode.info
│   │   │   ├── rna_mode.info
│   │   │   ├── rnaviral_mode.info
│   │   │   ├── sewage_mode.info
│   │   │   ├── simplification.info
│   │   │   └── toy.info
│   │   ├── final_contigs.fasta
│   │   ├── final_contigs.paths
│   │   ├── final.lib_data
│   │   ├── first_pe_contigs.fasta
│   │   ├── path_extend
│   │   ├── scaffolds.fasta
│   │   ├── scaffolds.paths
│   │   └── strain_graph.gfa
│   ├── misc
│   │   └── broken_scaffolds.fasta
│   ├── old2new_contig_names.tsv
│   ├── params.txt
│   ├── pipeline_state
│   │   ├── stage_0_before_start
│   │   ├── stage_1_as_start
│   │   ├── stage_2_k21
│   │   ├── stage_3_k33
│   │   ├── stage_4_k55
│   │   ├── stage_5_copy_files
│   │   ├── stage_6_as_finish
│   │   ├── stage_7_bs
│   │   └── stage_8_terminate
│   ├── run_spades.sh
│   ├── run_spades.yaml
│   ├── _final_contigs.fasta
│   ├── _prefilter_contigs.fasta
│   ├── scaffolds.fasta
│   ├── scaffolds.paths
│   ├── spades.log
│   ├── strain_graph.gfa
│   └── tmp
├── binning
│   └── vamb
│   ├── bins
│   │   └── _vamb_1.fasta
│   ├── checkm2
│   │   ├── checkm2.log
│   │   ├── diamond_output
│   │   └── protein_files
│   │   └── vamb_1.faa
│   ├── cluster_attribution.tsv
│   └── genome_stats.tsv
├── finished_assembly
├── logs
│   ├── assembly
│   │   ├── calculate_coverage
│   │   │   ├── align_reads_from_to_filtered_contigs.log
│   │   │   └── pilup_final_contigs.log
│   │   ├── post_process
│   │   │   ├── contig_stats_final.log
│   │   │   └── rename_and_filter_size.log
│   │   ├── pre_process
│   │   │   ├── error_correction_QC.log
│   │   │   └── merge_pairs_QC.errorcorr.log
│   │   └── spades.log
│   ├── binning
│   │   ├── get_bins_vamb.log
│   │   └── vamb
│   │   └── checkm2.log
│   ├── gene_annotation
│   │   └── prodigal.txt
│   ├── QC
│   │   ├── decontamination.err
│   │   ├── decontamination.log
│   │   ├── deduplicate.err
│   │   ├── deduplicate.log
│   │   ├── init.log
│   │   ├── quality_filter.err
│   │   ├── quality_filter.log
│   │   ├── read_stats
│   │   │   ├── clean.log
│   │   │   ├── deduplicated.log
│   │   │   ├── filtered.log
│   │   │   ├── QC.log
│   │   │   └── raw.log
│   │   └── stats
│   │   └── calculate_insert_size.log
│   └── _quality_filtering_stats.txt
├── sequence_alignment
│   └── .bam
└── sequence_quality_control
├── finished_QC
├── read_stats
│   ├── clean.zip
│   ├── deduplicated.zip
│   ├── filtered.zip
│   ├── QC_insert_size_hist.txt
│   ├── QC_read_length_hist.txt
│   ├── QC.zip
│   ├── raw.zip
│   └── read_counts.tsv
└── _decontamination_reference_stats.txt

51 directories, 166 files.

I am not closing the Issue just in case @SilasK would like to say this is completely wrong or not 😆