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tpellegrinetti / PGPg_finder

PGPg Finder is a command-line tool that offers different workflows for genome and metagenome annotation of Plant-Growth Promotion Genes. It's designed to be flexible and easy to use pipeline, with several pre-configured workflows to choose from based on the tools and steps you need.
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/bin/sh: 1: biom: not found and Lv2, Lv3, Lv4 no data for heatmaps #2

Open mike-bioinfo opened 4 months ago

mike-bioinfo commented 4 months ago

Hello! Thanks for this interesting tool, I have installed this tools through Miniconda and I just ran 1 metagenomics sample set (paired end fastq) in "metafast_wf" mode in which I have the next message just before the pipeline finished:

No data for Lv4 with Lv2=nan. Skipping heatmap. No data for Lv4 with Lv2=nan. Skipping heatmap. No data for Lv3 with Lv2=nan. Skipping heatmap. No data for Lv3 with Lv2=nan. Skipping heatmap. /bin/sh: 1: biom: not found [2024-07-31 18:31:44] Generated heatmaps

Which tool needs to be installed in order to avoid the "biom: not found" message?

And what does it mean Lv2, Lv3 and Lv4 during this "Skipping heatmap" message?

I have tried to run it using my assembly fasta file from the same fastq files but no success because it is complaning about option "-a" being illegal which is included in the command line like this:

python /home/bryan/raw_data_meta/SOFTWARE/PGPg_finder/PGPg_finder.py -w metafast_wf -i /home/bryan/raw_data_meta/FASTQ/ -a /home/bryan/raw_data_meta/2_assembly/test/ -o /home/bryan/raw_data_meta/2_assembly/test/fastway/ -t 16

/home/bryan/raw_data_meta/SOFTWARE/PGPg_finder/workflows/metafast_wf.sh: illegal option -- a Usage: /home/bryan/raw_data_meta/SOFTWARE/PGPg_finder/workflows/metafast_wf.sh -i -o -t [-m ]

Am I doing something wrong?. Any help would be really appreciated!

Thanks!

tpellegrinetti commented 3 months ago

Dear mike-bioinfo, thanks for reporting this errors and skrry for the delay.

Considering the biom problem it occurs because you need to install the biom package:

conda install -c conda-forge biom-format

The heatmap lv2 errors its normal, its only not generating graphs in lv2.

About the option -a I will check what is happening.