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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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Exit gracefully #21

Closed pbelmann closed 2 years ago

pbelmann commented 2 years ago

Thank you for developing this tool!

If all contigs are filtered out, for example due to short length, then Metacoag should end gracefully:

2022-07-04 13:49:45,194 - INFO - Welcome to MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs. 2022-07-04 13:49:45,195 - INFO - This version of MetaCoAG makes use of the assembly graph produced by SPAdes which is based on the de Bruijn graph approach. 2022-07-04 13:49:45,195 - INFO - Input arguments: 2022-07-04 13:49:45,195 - INFO - Assembler used: flye 2022-07-04 13:49:45,195 - INFO - Contigs file: contigs.fa.gz 2022-07-04 13:49:45,195 - INFO - Assembly graph file: nano_assembly_graph.gfa 2022-07-04 13:49:45,195 - INFO - Contig paths file: nano_assembly_info.txt 2022-07-04 13:49:45,195 - INFO - Abundance file: assembly_depth_final.tsv 2022-07-04 13:49:45,195 - INFO - Final binning output file: ./ 2022-07-04 13:49:45,195 - INFO - Marker file: /MetaCoAG/auxiliary/marker.hmm 2022-07-04 13:49:45,195 - INFO - Minimum length of contigs to consider: 1000 2022-07-04 13:49:45,195 - INFO - Depth to consider for label propagation: 10 2022-07-04 13:49:45,195 - INFO - p_intra: 0.1 2022-07-04 13:49:45,195 - INFO - p_inter: 0.01 2022-07-04 13:49:45,195 - INFO - mg_threshold: 0.5 2022-07-04 13:49:45,195 - INFO - bin_mg_threshold: 0.1 2022-07-04 13:49:45,195 - INFO - min_bin_size: 200000 base pairs 2022-07-04 13:49:45,195 - INFO - d_limit: 20 2022-07-04 13:49:45,195 - INFO - Number of threads: 28 2022-07-04 13:49:45,195 - INFO - MetaCoAG started 2022-07-04 13:49:45,212 - INFO - Total number of contigs available: 121 2022-07-04 13:49:45,219 - INFO - Total number of edges in the assembly graph: 188 2022-07-04 13:49:45,219 - INFO - Total isolated contigs in the assembly graph: 37 2022-07-04 13:49:45,219 - INFO - Obtaining lengths and coverage values of contigs Traceback (most recent call last): File "/MetaCoAG/src/metacoag_main.py", line 303, in abundance_file=abundance_file) File "/MetaCoAG/src/metacoag_utils/feature_utils.py", line 155, in get_cov_len n_samples = len(coverages[0]) KeyError: 0

Vini2 commented 2 years ago

Hello @pbelmann,

Thank you very much for your interest in MetaCoAG and for pointing out this error.