search

anuradhawick / LRBinner

LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.
https://doi.org/10.4230/LIPIcs.WABI.2021.11
GNU General Public License v2.0
28 stars 4 forks source link

Contigs binning -marker genes/hmmout problem #19

Open Nafson194 opened 4 months ago

Nafson194 commented 4 months ago

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'

anuradhawick commented 4 months ago

Hi thanks for getting in touch.

Could you check if these are available in your system?

Nafson194 commented 4 months ago

Hi @anuradhawick ,

Thank you for getting back to me.

I managed to run it successfully after installing the tool using conda. However, I have one more issues that I would like to clarify with you. I used metabat2 for binning of one sample and generated 7 bins. Later, this tool started running and produced only two bins from the same sample. Do you know any reason behind generating few bins compared to the software not designed purposely for binning of long reads sequences?

Best, Nafi'u

anuradhawick commented 4 months ago

I think LRBinner can give lesser number of bins for assemblies because I have not designed it for binning contigs.

On the other hand, contigs binning tools may have heuristics more applicable for contigs like accuracy. If it's using marker genes long reads might mislead the binner too.

Nafson194 commented 4 months ago

Thank you for the information. May I know if you know/have any other tool for binning of assemblies from long reads?

Maybe tools designed specifically for long reads binning would give a better genomes in terms of quality.

Thanks

anuradhawick commented 4 months ago

You could try this

https://github.com/metagentools/MetaCoAG

Nafson194 commented 4 months ago

Thank you for your response and recommendation.

On Thu, 21 Mar 2024 at 12:08, Anuradha @.***> wrote:

You could try this

https://github.com/metagentools/MetaCoAG

— Reply to this email directly, view it on GitHub https://github.com/anuradhawick/LRBinner/issues/19#issuecomment-2011962835, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR73D2L3CJNCKKZRMEU5SXTYZK5UTAVCNFSM6AAAAABD4FAPFGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJRHE3DEOBTGU . You are receiving this because you authored the thread.Message ID: @.***>