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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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External bins #767

Closed lokyimandy closed 5 months ago

lokyimandy commented 6 months ago

Hello! Thank you for creating such a useful tool. I want to use the bins created from a previous SqueezeMeta project to calculate their coverage and TPM in other set of samples, without going through the assembly and binning processes again. I would like to ask if it is correct that I only add the -extbins option in a new project as below? Thanks.

SqueezeMeta.pl -m coassembly -p project name -s /path/samplesfile -f /path/reads directory -t 40 -extbins /path/bins directory

fpusan commented 6 months ago

Yes, It works like that. However this is only present in our development versión (squeezemeta-dev conda package)

lokyimandy commented 5 months ago

I tried to install the squeezemeta-dev conda package with mamba run, and it reported _SafetyError: The package for squeezemeta-dev located at /envs/pkgs/squeezemeta-dev-1.7.0.alpha5-py310pl5262r41_0 appears to be corrupted. The path 'SqueezeMeta/scripts/SqueezeMeta_conforiginal.pl' has an incorrect size. reported size: 8147 bytes actual size: 0 bytes

And the ./test_install.pl returns many error as shown in the attachment. test run result.docx

fpusan commented 5 months ago

This seems related to your conda installation in particular. Maybe try clearing the conda cache, or installing under a new miniconda3 install.

lokyimandy commented 5 months ago

Thank you for the advices. The installation is complete and the testing is alright after I update the Conda and reinstall mamba.

fpusan commented 5 months ago

Glad to hear. Closing issue