Error in rule binny

[Valentin-Bio]

Hello developer, I have experienced the following error message after running binny:

Finished job 5.
1 of 3 steps (33%) done
Select jobs to execute...

[Mon Nov 10 18:45:44 2025]
Job 1: binny: Running Python Binny.
Reason: Missing output files: /home/vberrios/comau/remastered_mags/binny_bins/binny.done; Input files updated by another job: /home/vberrios/comau/remastered_mags/binny_bins/intermediary/mantis_out/consensus_annotation.tsv

/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/bin/python3.10 /home/vberrios/comau/remastered_mags/binny_bins/.snakemake/scripts/tmpdmwq2wiu.binny.py
Traceback (most recent call last):
File "/home/vberrios/comau/remastered_mags/binny_bins/.snakemake/scripts/tmpdmwq2wiu.binny.py", line 220, in
binny()
File "/home/vberrios/comau/remastered_mags/binny_bins/.snakemake/scripts/tmpdmwq2wiu.binny.py", line 169, in binny
all_good_bins, contig_data_df_org, min_purity = iterative_embedding(x_contigs, depth_dict, all_good_bins, starting_completeness,
File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/site-packages/binny/binning.py", line 498, in iterative_embedding
round_x_depth = np.array([depth_dict[contig] for contig in round_x_contigs])
File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/site-packages/binny/binning.py", line 498, in
round_x_depth = np.array([depth_dict[contig] for contig in round_x_contigs])
KeyError: 'BAC4A_k141_155028.23590 flag=0 multi=30.9991 len=785457'
[Mon Nov 10 19:05:31 2025]
Error in rule binny:
jobid: 1
input: /home/vberrios/comau/remastered_mags/binny_bins/intermediary/assembly.contig_depth.txt, /home/vberrios/comau/remastered_mags/binny_bins/intermediary/annotation.filt.gff, /home/vberrios/comau/remastered_mags/binny_bins/intermediary/assembly.formatted.fa, /home/vberrios/comau/remastered_mags/binny_bins/intermediary/mantis_out/consensus_annotation.tsv
output: /home/vberrios/comau/remastered_mags/binny_bins/binny.done
log: /home/vberrios/comau/remastered_mags/binny_bins/logs/binning_binny.log (check log file(s) for error details)

RuleException:
CalledProcessError in file /opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/site-packages/binny/Snakefile, line 367:
Command 'set -euo pipefail; /opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/bin/python3.10 /home/vberrios/comau/remastered_mags/binny_bins/.snakemake/scripts/tmpdmwq2wiu.binny.py' returned non-zero exit status 1.
File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/site-packages/binny/Snakefile", line 367, in __rule_binny
File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-11-10T102451.761152.snakemake.log

This is the code I used:

conda activate binny_env

binny \
  --assembly /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta  \
  --contig_depth /home/vberrios/comau/reads/bam_files/sorted_bam/depth_comau.txt \
  --outputdir /home/vberrios/comau/remastered_mags/binny_bins \
  --threads 40 \
  --tmp_dir /home/vberrios/comau/remastered_mags/binny_tmp 

[ohickl]

Hi,
I think its because there are spaces in the contig fasta headers. could you ensure that both in unique_contigs.fasta and and depth_comau.txt you replace them with e.g. _? you could do:

sed -i.bak 's|\s|_|g' /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta /home/vberrios/comau/reads/bam_files/sorted_bam/depth_comau.txt

[Valentin-Bio]

Thanks so much, I will change that on the contigs names, in addition, is there any flag of the program to retake the program from a checkpoint or should I run it from the beginning ?

[Valentin-Bio]

Ok I have experienced another error message in the same part, but now it seems that BInny is trying to convert the second column of the depth file (contigLen) to Float:

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/vberrios/comau/remastered_mags/binny_bins/.snakemake/scripts/tmp9j_t2ez5.binny.py", line 220, in
binny()
File "/home/vberrios/comau/remastered_mags/binny_bins/.snakemake/scripts/tmp9j_t2ez5.binny.py", line 169, in binny
all_good_bins, contig_data_df_org, min_purity = iterative_embedding(x_contigs, depth_dict, all_good_bins, starting_completeness,
File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/site-packages/binny/binning.py", line 612, in iterative_embedding
contig_data_df = load_and_merge_cont_data(annot_file, mg_depth_file, coord_df, dims=n_dim,
File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/site-packages/binny/utils.py", line 85, in load_and_merge_cont_data
depth_df = pd.read_csv(depth_file, sep='\t', low_memory=False, names=depth_cols, dtype=depth_dtype_dict)
File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 626, in _read
return parser.read(nrows)
File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1923, in read
) = self._engine.read( # type: ignore[attr-defined]
File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 239, in read
data = self._reader.read(nrows)
File "pandas/_libs/parsers.pyx", line 820, in pandas._libs.parsers.TextReader.read
File "pandas/_libs/parsers.pyx", line 921, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 1066, in pandas._libs.parsers.TextReader._convert_column_data
File "pandas/_libs/parsers.pyx", line 1167, in pandas._libs.parsers.TextReader._convert_tokens
ValueError: could not convert string to float: 'contigLen'
[Wed Nov 12 05:35:01 2025]
Error in rule binny:
jobid: 1
input: /home/vberrios/comau/remastered_mags/binny_bins/intermediary/assembly.contig_depth.txt, /home/vberrios/comau/remastered_mags/binny_bins/intermediary/annotation.filt.gff, /home/vberrios/comau/remastered_mags/binny_bins/intermediary/assembly.formatted.fa, /home/vberrios/comau/remastered_mags/binny_bins/intermediary/mantis_out/consensus_annotation.tsv
output: /home/vberrios/comau/remastered_mags/binny_bins/binny.done
log: /home/vberrios/comau/remastered_mags/binny_bins/logs/binning_binny.log (check log file(s) for error details)

RuleException:
CalledProcessError in file /opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/site-packages/binny/Snakefile, line 367:
Command 'set -euo pipefail; /opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/bin/python3.10 /home/vberrios/comau/remastered_mags/binny_bins/.snakemake/scripts/tmp9j_t2ez5.binny.py' returned non-zero exit status 1.
File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/site-packages/binny/Snakefile", line 367, in __rule_binny
File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/binny_env/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-11-11T133213.896814.snakemake.log

with this, the column names of the depth file must be: [contigname, sample1, sample2, ... sampleN] ?