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Vini2 / phables

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
https://phables.readthedocs.io/
MIT License
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[Feature request] Support for long-read data #8

Closed Vini2 closed 5 months ago

Vini2 commented 1 year ago

Is your feature request related to a problem? Please describe. Currently, long-read data are not fully utilised by phables.

Describe the solution you'd like Allow the option to select between long-read and short-read data when running phables.

Points to note in development Keep track of unitigs aligning to long reads and create relevant subpaths with read counts.

alegarritano commented 7 months ago

Hi @Vini2,

Thanks for developing the tools, it seems very promising. Unfortunately, I am facing an error when trying to run it. "phables test" runs fine, but I am trying to use it with long-read data, and the software crashes just after I run it.

I noticed that you say long-read data is not fully utilised, but I am wondering if the software is compatible with long-read data at the moment and some information is not used or if it's not compatible at all and this is a glitch on my end.

This is the error:

[2023:12:07 21:50:46] --------------------- [2023:12:07 21:50:46] | Snakemake command | [2023:12:07 21:50:46] ---------------------

snakemake -s mypython3env_Phables/lib/python3.11/site-packages/phables/workflow/phables.smk --configfile phables.out/config.yaml --cores 36 --use-conda --conda-prefix mypython3env_Phables/lib/python3.11/site-packages/phables/workflow/conda --rerun-incomplete --printshellcmds --nolock --show-failed-logs Set parameter WLSAccessID Set parameter WLSSecret Set parameter LicenseID to value 2450061 Academic license 2450061 - for non-commercial use only - registered to al___@unsw.edu.au mypython3env_Phables/lib/python3.11/site-packages/pulp/apis/gurobi_api.py:170: UserWarning: GUROBI error: Unknown parameter '_test'. warnings.warn("GUROBI error: {}.".format(e)) Config file mypython3env_Phables/lib/python3.11/site-packages/phables/workflow/../config/config.yaml is extended by additional config specified via the command line. Config file mypython3env_Phables/lib/python3.11/site-packages/phables/workflow/../config/databases.yaml is extended by additional config specified via the command line. Output files will be saved to directory, phables.out

IndexError in file mypython3env_Phables/lib/python3.11/site-packages/phables/workflow/rules/02_phables_preflight.smk, line 23: list index out of range File "mypython3env_Phables/lib/python3.11/site-packages/phables/workflow/phables.smk", line 16, in File "mypython3env_Phables/lib/python3.11/site-packages/phables/workflow/rules/02_phables_preflight.smk", line 23, in File "mypython3env_Phables/lib/python3.11/site-packages/metasnek/fastq_finder.py", line 196, in parse_samples_to_dictionary File "mypython3env_Phables/lib/python3.11/site-packages/metasnek/fastq_finder.py", line 140, in parse_samples File "mypython3env_Phables/lib/python3.11/site-packages/metasnek/fastq_finder.py", line 95, in parse_tsv_file

Thanks,

Vini2 commented 7 months ago

Hi @alegarritano,

Thanks for your interest in Phables.

Currently Phables does not support long-read data. I'm planning to add support in the next few months. I'll let you know once it's implemented.

Thanks!