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metagentools / MetaCoAG

🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
https://metacoag.readthedocs.io/en/stable/
GNU General Public License v3.0
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Cannot find FragGeneScan #43

Closed bheimbu closed 2 months ago

bheimbu commented 4 months ago

Hello,

I've installed MetaCoAG 1.1.4 with mamba but it cannot find run_FragGeneScan.pl, while it is present. I've not experienced something like this before. 

$ mamba activate mags
(mags)$ which run_FragGeneScan.pl 
/home/uni08/bheimbu/miniforge3/envs/mags/bin/run_FragGeneScan.pl

I've no idea what's going here.

2024-04-09 11:54:50,795 - INFO - Welcome to MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs.
2024-04-09 11:54:50,796 - INFO - Input arguments: 
2024-04-09 11:54:50,796 - INFO - Assembler used: megahit
2024-04-09 11:54:50,796 - INFO - Contigs file: results_paired_end/assemblies/preprocessed_contigs/BEC327/BEC327.fna
2024-04-09 11:54:50,796 - INFO - Assembly graph file: results_paired_end/MAGs/metacoag/BEC327/BEC327.gfa
2024-04-09 11:54:50,796 - INFO - Contig paths file: None
2024-04-09 11:54:50,796 - INFO - Abundance file: results_paired_end/MAGs/metacoag/BEC327/BEC327.abundance.tsv
2024-04-09 11:54:50,796 - INFO - Final binning output file: results_paired_end/MAGs/metacoag/BEC327
2024-04-09 11:54:50,797 - INFO - Marker gene file hmm: auxiliary/marker.hmm
2024-04-09 11:54:50,797 - INFO - Minimum length of contigs to consider: 1000
2024-04-09 11:54:50,797 - INFO - Depth to consider for label propagation: 10
2024-04-09 11:54:50,797 - INFO - p_intra: 0.1
2024-04-09 11:54:50,797 - INFO - p_inter: 0.01
2024-04-09 11:54:50,797 - INFO - Do not use --cut_tc: False
2024-04-09 11:54:50,797 - INFO - mg_threshold: 0.5
2024-04-09 11:54:50,797 - INFO - bin_mg_threshold: 0.33333
2024-04-09 11:54:50,797 - INFO - min_bin_size: 200000 base pairs
2024-04-09 11:54:50,797 - INFO - d_limit: 20
2024-04-09 11:54:50,798 - INFO - Number of threads: 20
2024-04-09 11:54:50,798 - INFO - MetaCoAG started
2024-04-09 11:54:50,901 - INFO - Total number of contigs available: 2013
2024-04-09 11:54:50,903 - INFO - Total number of edges in the assembly graph: 33
2024-04-09 11:54:50,910 - INFO - Total isolated contigs in the assembly graph: 1952
2024-04-09 11:54:50,910 - INFO - Obtaining lengths and coverage values of contigs
2024-04-09 11:54:50,961 - INFO - Total long contigs: 2013
2024-04-09 11:54:50,961 - INFO - Total isolated long contigs in the assembly graph: 1952
2024-04-09 11:54:50,961 - INFO - Obtaining tetranucleotide frequencies of contigs
2024-04-09 11:54:51,008 - INFO - Scanning for single-copy marker genes
2024-04-09 11:54:51,008 - ERROR - FragGeneScan does not exist. Please install from https://omics.informatics.indiana.edu/FragGeneScan/

Cheers Bastian

Vini2 commented 2 months ago

Hi @bheimbu,

So sorry about the delay in getting back to you. Can you let me know the specs of your machine? Also, can you try running the latest version of MetaCoAG?

Thanks, Vijini

bheimbu commented 2 months ago

Hi @Vini2,

it was a misconfig from my side. Loaded the wrong conda environment, so problem is solved.

Cheers Bastian