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I got a have been using MetaCoAG for a while, works well most of the time until I got a KeyError: contig_4488. The dataset Ive been working on is ONT, assembled on metaFlye.
This contig_4488 is not present in my flye assembly. An edge_4488 was present in the graph assembly though (Could this be the issue?).
2024-03-27 02:39:34,410 - INFO - Welcome to MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs.
2024-03-27 02:39:34,429 - INFO - Input arguments:
2024-03-27 02:39:34,430 - INFO - Assembler used: flye
2024-03-27 02:39:34,430 - INFO - Contigs file: /fs03/jm41/Zarul/C002_D1_results/flye/assembly.fasta
2024-03-27 02:39:34,430 - INFO - Assembly graph file: /fs03/jm41/Zarul/C002_D1_results/flye/assembly_graph.gfa
2024-03-27 02:39:34,430 - INFO - Contig paths file: /fs03/jm41/Zarul/C002_D1_results/flye/assembly_info.txt
2024-03-27 02:39:34,430 - INFO - Abundance file: /fs03/jm41/Zarul/C002_D1_results/binning_medaka/metacoag/coverm_abundance.tsv
2024-03-27 02:39:34,430 - INFO - Final binning output file: /fs03/jm41/Zarul/C002_D1_results/binning_medaka/metacoag
2024-03-27 02:39:34,430 - INFO - Marker gene file hmm: auxiliary/marker.hmm
2024-03-27 02:39:34,430 - INFO - Minimum length of contigs to consider: 1000
2024-03-27 02:39:34,430 - INFO - Depth to consider for label propagation: 10
2024-03-27 02:39:34,431 - INFO - p_intra: 0.1
2024-03-27 02:39:34,431 - INFO - p_inter: 0.01
2024-03-27 02:39:34,431 - INFO - Do not use --cut_tc: False
2024-03-27 02:39:34,431 - INFO - mg_threshold: 0.5
2024-03-27 02:39:34,431 - INFO - bin_mg_threshold: 0.33333
2024-03-27 02:39:34,431 - INFO - min_bin_size: 200000 base pairs
2024-03-27 02:39:34,431 - INFO - d_limit: 20
2024-03-27 02:39:34,431 - INFO - Number of threads: 8
2024-03-27 02:39:34,431 - INFO - MetaCoAG started
2024-03-27 02:39:53,232 - INFO - Total number of contigs available: 269678
2024-03-27 02:39:58,801 - INFO - Total number of edges in the assembly graph: 77552
2024-03-27 02:39:58,928 - INFO - Total isolated contigs in the assembly graph: 244283
2024-03-27 02:39:58,929 - INFO - Obtaining lengths and coverage values of contigs
2024-03-27 02:40:18,190 - INFO - Total long contigs: 267613
2024-03-27 02:40:18,190 - INFO - Total isolated long contigs in the assembly graph: 243244
2024-03-27 02:40:18,191 - INFO - Obtaining tetranucleotide frequencies of contigs
2024-03-27 02:47:08,567 - INFO - Scanning for single-copy marker genes
2024-03-27 02:47:08,636 - INFO - .hmmout file already exists
2024-03-27 02:47:08,636 - INFO - Obtaining contigs with single-copy marker genes
Traceback (most recent call last):
File "/home/mzar0002/miniconda3/envs/metacoag_/bin/metacoag", line 1260, in <module>
main()
File "/fs03/jm41/Zarul/envs/metacoag/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs03/jm41/Zarul/envs/metacoag/lib/python3.12/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/fs03/jm41/Zarul/envs/metacoag/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs03/jm41/Zarul/envs/metacoag/lib/python3.12/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mzar0002/miniconda3/envs/metacoag_/bin/metacoag", line 613, in main
) = marker_gene_utils.get_contigs_with_marker_genes(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs03/jm41/Zarul/envs/metacoag/lib/python3.12/site-packages/metacoag_utils/marker_gene_utils.py", line 147, in get_contigs_with_marker_genes
contig_num = contig_names_rev[contig_name]
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
KeyError: 'contig_4488'
Thank you 🙏
The text was updated successfully, but these errors were encountered:
Hello Vini,
I got a have been using MetaCoAG for a while, works well most of the time until I got a
KeyError: contig_4488. The dataset Ive been working on is ONT, assembled on metaFlye.This contig_4488 is not present in my flye assembly. An edge_4488 was present in the graph assembly though (Could this be the issue?).
As you can see, "contig_4488" is supposedly not present in any of the input files given to MetaCoAG.
The command executed:
Here is the error message:
Thank you 🙏
The text was updated successfully, but these errors were encountered: