Segmentation fault?

[Valentin-Bio]

Hello dear developer, I have installed metabinner via the conda recipe, after running some hours I had an error mesager. This is the command I used:

#!/bin/bash

#SBATCH -J metabinner
#SBATCH -e metabinner.err
#SBATCH -o metabinner.out
#SBATCH --partition=basic
#SBATCH --cpus-per-task=40


module load Miniconda


conda activate metabinner_env


#path to MetaBinner
metabinner_path=/opt/miniconda/miniconda-py312_24.3.0-0/envs/metabinner_env/bin
Note: If users install MetaBinner via bioconda, they can set metabinner_path as follows: metabinner_path=$(dirname $(which run_metabinner.sh))

##test data
#path to the input files for MetaBinner and the output dir:
contig_file=/home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta
output_dir=/home/vberrios/comau/remastered_mags/metabinner_bins
coverage_profiles=/home/vberrios/comau/reads/bam_files/sorted_bam/depth_comau_2meetabinner.txt
kmer_profile=/home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs_kmer_4_f1000.csv


bash run_metabinner.sh -a ${contig_file} -o ${output_dir} -d ${coverage_profiles} -k ${kmer_profile} -p ${metabinner_path} -t 40

and this is part of the error message:

2025-10-24 11:11:17,377 - Input arguments:
2025-10-24 11:11:17,377 - Contig_file:  /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta
2025-10-24 11:11:17,377 - Coverage_profiles:    /home/vberrios/comau/reads/bam_files/sorted_bam/depth_comau_2meetabinner.txt
2025-10-24 11:11:17,377 - Composition_profiles: /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs_kmer_4_f1000.csv
2025-10-24 11:11:17,377 - Output file path:     /home/vberrios/comau/remastered_mags/metabinner_bins/metabinner_res/result.tsv
2025-10-24 11:11:17,377 - Predefined Clusters:  Auto
2025-10-24 11:11:17,377 - The number of threads:        40
2025-10-24 11:12:21,391 - The number of contigs:        1709698
2025-10-24 11:12:21,391 - gen bacar marker seed
[vberrios@maccartney-front comau]$ head -n 50 metabinner.err
/var/spool/slurmd/job27068/slurm_script: line 18: Note:: command not found
2025-10-24 11:11:17,377 - Input arguments:
2025-10-24 11:11:17,377 - Contig_file:  /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta
2025-10-24 11:11:17,377 - Coverage_profiles:    /home/vberrios/comau/reads/bam_files/sorted_bam/depth_comau_2meetabinner.txt
2025-10-24 11:11:17,377 - Composition_profiles: /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs_kmer_4_f1000.csv
2025-10-24 11:11:17,377 - Output file path:     /home/vberrios/comau/remastered_mags/metabinner_bins/metabinner_res/result.tsv
2025-10-24 11:11:17,377 - Predefined Clusters:  Auto
2025-10-24 11:11:17,377 - The number of threads:        40
2025-10-24 11:12:21,391 - The number of contigs:        1709698
2025-10-24 11:12:21,391 - gen bacar marker seed
2025-10-24 11:12:21,392 - exec cmd: run_FragGeneScan.pl -genome=/home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta -out=/home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.frag -complete=0 -train=complete -thread=40 1>/home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.frag.out 2>/home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.frag.err
2025-10-24 11:30:31,147 - exec cmd: hmmsearch --domtblout /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.bacar_marker.hmmout --cut_tc --cpu 40 /opt/miniconda/miniconda-py312_24.3.0-0/envs/metabinner_env/bin/scripts/../auxiliary/bacar_marker.hmm /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.frag.faa 1>/home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.bacar_marker.hmmout.out 2>/home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.bacar_marker.hmmout.err
2025-10-24 11:38:48,896 - exec cmd: /opt/miniconda/miniconda-py312_24.3.0-0/envs/metabinner_env/bin/scripts/../auxiliary/test_getmarker_1quarter.pl /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.bacar_marker.hmmout /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta 1001 /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.bacar_marker.1quarter_lencutoff_1001.seed
2025-10-24 11:39:18,984 - bacar_marker_1quarter_seed_num:       2636
2025-10-24 11:39:18,984 - exec cmd: /opt/miniconda/miniconda-py312_24.3.0-0/envs/metabinner_env/bin/scripts/../auxiliary/test_getmarker_2quarter.pl /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.bacar_marker.hmmout /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta 1001 /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.bacar_marker.2quarter_lencutoff_1001.seed
2025-10-24 11:39:48,894 - bacar_marker_2quarter_seed_num:       2774
2025-10-24 11:39:48,894 - exec cmd: /opt/miniconda/miniconda-py312_24.3.0-0/envs/metabinner_env/bin/scripts/../auxiliary/test_getmarker_3quarter.pl /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.bacar_marker.hmmout /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta 1001 /home/vberrios/comau/reads/assemblies/all_contigs/all_guys/unique_contigs.fasta.bacar_marker.3quarter_lencutoff_1001.seed
2025-10-24 11:40:19,024 - bacar_marker_3quarter_seed_num:       2906
2025-10-24 11:40:19,024 - start calculate contig length
2025-10-24 11:40:49,862 - Dataset scale:        large
2025-10-24 11:40:56,344 - start estimate_bin_number
Traceback (most recent call last):
  File "./component_binning.py", line 476, in <module>
    bin_number = estimate_bin_number(X_t, candK, dataset_scale=dataset_scale, len_weight=length_weight)
  File "./component_binning.py", line 162, in estimate_bin_number
    kmeans.fit(X_mat, sample_weight=len_weight)
  File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/metabinner_env/lib/python3.7/site-packages/sklearn/cluster/_kmeans.py", line 956, in fit
    for seed in seeds)
  File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/metabinner_env/lib/python3.7/site-packages/joblib/parallel.py", line 1952, in __call__
    return output if self.return_generator else list(output)
  File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/metabinner_env/lib/python3.7/site-packages/joblib/parallel.py", line 1595, in _get_outputs
    yield from self._retrieve()
  File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/metabinner_env/lib/python3.7/site-packages/joblib/parallel.py", line 1699, in _retrieve
    self._raise_error_fast()
  File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/metabinner_env/lib/python3.7/site-packages/joblib/parallel.py", line 1734, in _raise_error_fast
    error_job.get_result(self.timeout)
  File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/metabinner_env/lib/python3.7/site-packages/joblib/parallel.py", line 736, in get_result
    return self._return_or_raise()
  File "/opt/miniconda/miniconda-py312_24.3.0-0/envs/metabinner_env/lib/python3.7/site-packages/joblib/parallel.py", line 754, in _return_or_raise
    raise self._result
joblib.externals.loky.process_executor.TerminatedWorkerError: A worker process managed by the executor was unexpectedly terminated. This could be caused by a segmentation fault while calling the function or by an excessive memory usage causing the Operating System to kill the worker.

The exit codes of the workers are {SIGKILL(-9)}

real    116m56.783s
user    2525m11.168s
sys     163m20.755s
/home/vberrios/comau/reads/bam_files/sorted_bam/depth_comau_2meetabinner.txt: line 1: contigname: command not found
/home/vberrios/comau/reads/bam_files/sorted_bam/depth_comau_2meetabinner.txt: line 2: BAC4A_k141_316728.1: command not found
/home/vberrios/comau/reads/bam_files/sorted_bam/depth_comau_2meetabinner.txt: line 3: BAC4A_k141_253384.2: command not found

what could be wrong here?

bests,

Valentín.

[jarrodscott]

I am having a similar issue. I installed using the conda recipe.

Metabinner is trying to execute helper scripts that should live in $CONDA_PREFIX/auxiliary/ but there is no such directory in the conda build. For me test_getmarker_1quarter.pl lives here:

~/miniconda3/envs/metabinner/bin/auxiliary/test_getmarker_1quarter.pl
~/miniconda3/envs/metabinner/bin/test_getmarker_1quarter.pl

Instead metabinner is looking here ~/miniconda3/envs/metabinner/auxiliary/ which does not exist. So I guess one could create this directory and copy needed files there. I do not like this option because I will never remember what I did. Or try Installing MetaBinner via source code

[jarrodscott]

I can report that installing from source code produced similar errors :(

[Valentin-Bio]

I noticed it is a memory issue, after decreasing the number of threads (from 40 to 16), there is less memory usage and by far I have not seen an error message after the "start estimate_bin_number" step. Still I have to confirm the program finishes without errors.