Contigs binning -marker genes/hmmout problem

[Nafson194]

Hi @anuradhawick,

I am running LRBinner for ONT contigs generated from metaFlye. I would like to bin the contigs and come across this tool for binning of long reads data, however, I am running in the error indicating a missing file.

Could please give a helping hand on how to solve the problem?

Best, Nafi'u

here is the command I ran and error produced command: /tools/LRBinner/lrbinner.py contigs --reads-path Porechop/sample01.fastq --contigs final_assembly/sample01.assembly.fasta --output binning/

2024-02-27 14:29:48,189 - INFO - Computing contig lengths 2024-02-27 14:29:48,245 - INFO - Searching for marker genes Traceback (most recent call last): File "/lustre/groups/comi/tools/LRBinner/lrbinner.py", line 203, in main() File "/lustre/groups/comi/tools/LRBinner/lrbinner.py", line 185, in main pipelines.run_contig_binning(args) File "/lustre/groups/comi/tools/LRBinner/mbcclr_utils/pipelines.py", line 79, in run_contig_binning marker_gene_utils.get_contigs_with_marker_genes(output, 0.5, contig_length, 1000) File "/lustre/groups/comi/tools/LRBinner/metacoag_utils/marker_gene_utils.py", line 55, in get_contigs_with_marker_genes with open(f"{output}/marker_genes/contigs.hmmout", "r") as myfile: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

FileNotFoundError: [Errno 2] No such file or directory: '07_binning/marker_genes/contigs.hmmout'