2026-06-05 07:11:22 INFO:	***** Start a BUSCO v6.1.0 analysis, current time: 06/05/2026 07:11:22 *****
2026-06-05 07:11:22 INFO:	Configuring BUSCO with local environment
2026-06-05 07:11:22 WARNING:	Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.
2026-06-05 07:11:22 INFO:	Running genome mode
2026-06-05 07:11:22 INFO:	'Force' option selected; overwriting previous results directory
2026-06-05 07:11:22 INFO:	Downloading information on latest versions of BUSCO data...
2026-06-05 07:11:23 INFO:	Input file is /busco_wd/test_data/bacteria/genome.fna
2026-06-05 07:11:23 INFO:	No lineage specified. Running lineage auto selector.

2026-06-05 07:11:23 INFO:	***** Starting Auto Select Lineage *****
	This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
	--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
	A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
2026-06-05 07:11:23 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/archaea_odb12.2.2026-05-22.tar.gz'
2026-06-05 07:11:24 INFO:	Decompressing file '/busco_wd/busco_downloads/lineages/archaea_odb12.2.tar.gz'
2026-06-05 07:11:26 INFO:	Running BUSCO using lineage dataset archaea_odb12.2 (prokaryota, 2026-05-22)
2026-06-05 07:11:26 INFO:	Running 1 job(s) on bbtools, starting at 06/05/2026 07:11:26
2026-06-05 07:11:27 INFO:	[bbtools]	1 of 1 task(s) completed
2026-06-05 07:11:27 INFO:	***** Run Prodigal on input to predict and extract genes *****
2026-06-05 07:11:27 INFO:	Running Prodigal with genetic code 11 in single mode
2026-06-05 07:11:27 INFO:	Running 1 job(s) on prodigal, starting at 06/05/2026 07:11:27
2026-06-05 07:11:29 INFO:	[prodigal]	1 of 1 task(s) completed
2026-06-05 07:11:29 INFO:	Genetic code 11 selected as optimal
2026-06-05 07:11:29 INFO:	***** Run HMMER on gene sequences *****
2026-06-05 07:11:29 INFO:	Running 195 job(s) on hmmsearch, starting at 06/05/2026 07:11:29
2026-06-05 07:11:30 INFO:	[hmmsearch]	20 of 195 task(s) completed
2026-06-05 07:11:30 INFO:	[hmmsearch]	39 of 195 task(s) completed
2026-06-05 07:11:30 INFO:	[hmmsearch]	59 of 195 task(s) completed
2026-06-05 07:11:30 INFO:	[hmmsearch]	78 of 195 task(s) completed
2026-06-05 07:11:30 INFO:	[hmmsearch]	98 of 195 task(s) completed
2026-06-05 07:11:30 INFO:	[hmmsearch]	117 of 195 task(s) completed
2026-06-05 07:11:30 INFO:	[hmmsearch]	137 of 195 task(s) completed
2026-06-05 07:11:30 INFO:	[hmmsearch]	156 of 195 task(s) completed
2026-06-05 07:11:30 INFO:	[hmmsearch]	176 of 195 task(s) completed
2026-06-05 07:11:30 INFO:	[hmmsearch]	195 of 195 task(s) completed
2026-06-05 07:11:30 INFO:	Results:	C:4.6%[S:4.6%,D:0.0%],F:1.0%,M:94.4%,n:195	   

2026-06-05 07:11:30 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb12.2.2026-05-22.tar.gz'
2026-06-05 07:11:34 INFO:	Decompressing file '/busco_wd/busco_downloads/lineages/bacteria_odb12.2.tar.gz'
2026-06-05 07:11:36 INFO:	Running BUSCO using lineage dataset bacteria_odb12.2 (prokaryota, 2026-05-22)
2026-06-05 07:11:36 INFO:	Skipping BBTools as already run
2026-06-05 07:11:36 INFO:	***** Run Prodigal on input to predict and extract genes *****
2026-06-05 07:11:36 INFO:	Genetic code 11 selected as optimal
2026-06-05 07:11:36 INFO:	***** Run HMMER on gene sequences *****
2026-06-05 07:11:36 INFO:	Running 116 job(s) on hmmsearch, starting at 06/05/2026 07:11:36
2026-06-05 07:11:37 INFO:	[hmmsearch]	12 of 116 task(s) completed
2026-06-05 07:11:37 INFO:	[hmmsearch]	24 of 116 task(s) completed
2026-06-05 07:11:37 INFO:	[hmmsearch]	35 of 116 task(s) completed
2026-06-05 07:11:37 INFO:	[hmmsearch]	47 of 116 task(s) completed
2026-06-05 07:11:37 INFO:	[hmmsearch]	58 of 116 task(s) completed
2026-06-05 07:11:37 INFO:	[hmmsearch]	70 of 116 task(s) completed
2026-06-05 07:11:37 INFO:	[hmmsearch]	82 of 116 task(s) completed
2026-06-05 07:11:37 INFO:	[hmmsearch]	93 of 116 task(s) completed
2026-06-05 07:11:37 INFO:	[hmmsearch]	105 of 116 task(s) completed
2026-06-05 07:11:38 INFO:	[hmmsearch]	116 of 116 task(s) completed
2026-06-05 07:11:38 INFO:	Results:	C:20.7%[S:20.7%,D:0.0%],F:1.7%,M:77.6%,n:116	   

2026-06-05 07:11:38 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb12.2.2026-05-13.tar.gz'
2026-06-05 07:11:48 INFO:	Decompressing file '/busco_wd/busco_downloads/lineages/eukaryota_odb12.2.tar.gz'
2026-06-05 07:11:51 INFO:	Running BUSCO using lineage dataset eukaryota_odb12.2 (eukaryota, 2026-05-13)
2026-06-05 07:11:51 INFO:	Skipping BBTools as already run
2026-06-05 07:11:51 INFO:	Running 1 job(s) on miniprot_index, starting at 06/05/2026 07:11:51
2026-06-05 07:11:51 INFO:	[miniprot_index]	1 of 1 task(s) completed
2026-06-05 07:11:55 INFO:	Running 1 job(s) on miniprot_align, starting at 06/05/2026 07:11:55
2026-06-05 07:13:21 INFO:	[miniprot_align]	1 of 1 task(s) completed
2026-06-05 07:13:28 INFO:	***** Run HMMER on gene sequences *****
2026-06-05 07:13:28 INFO:	Running 99 job(s) on hmmsearch, starting at 06/05/2026 07:13:28
2026-06-05 07:13:28 INFO:	[hmmsearch]	10 of 99 task(s) completed
2026-06-05 07:13:28 INFO:	[hmmsearch]	20 of 99 task(s) completed
2026-06-05 07:13:28 INFO:	[hmmsearch]	30 of 99 task(s) completed
2026-06-05 07:13:28 INFO:	[hmmsearch]	40 of 99 task(s) completed
2026-06-05 07:13:29 INFO:	[hmmsearch]	50 of 99 task(s) completed
2026-06-05 07:13:29 INFO:	[hmmsearch]	60 of 99 task(s) completed
2026-06-05 07:13:29 INFO:	[hmmsearch]	70 of 99 task(s) completed
2026-06-05 07:13:29 INFO:	[hmmsearch]	80 of 99 task(s) completed
2026-06-05 07:13:29 INFO:	[hmmsearch]	90 of 99 task(s) completed
2026-06-05 07:13:29 INFO:	[hmmsearch]	99 of 99 task(s) completed
2026-06-05 07:13:29 INFO:	4 exons in total
2026-06-05 07:13:29 WARNING:	1 of 2 Complete matches (50.0%) contain internal stop codons in Miniprot gene predictions
2026-06-05 07:13:29 WARNING:	BUSCO gene predictions from Miniprot have low average identity (0.29). You may want to repeat the analysis using the Metaeuk pipeline.
2026-06-05 07:13:29 INFO:	Results:	C:1.6%[S:1.6%,D:0.0%],F:0.0%,M:98.4%,n:125,E:50.0%	   

2026-06-05 07:13:29 INFO:	bacteria_odb12.2 selected

2026-06-05 07:13:29 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2026-06-05 07:13:29 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.bacteria_odb12.2.2026-05-27.txt.tar.gz'
2026-06-05 07:13:29 INFO:	Decompressing file '/busco_wd/busco_downloads/placement_files/list_of_reference_markers.bacteria_odb12.2.2026-05-27.txt.tar.gz'
2026-06-05 07:13:29 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/tree.bacteria_odb12.2.2026-05-27.nwk.tar.gz'
2026-06-05 07:13:30 INFO:	Decompressing file '/busco_wd/busco_downloads/placement_files/tree.bacteria_odb12.2.2026-05-27.nwk.tar.gz'
2026-06-05 07:13:30 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.bacteria_odb12.2.2026-05-27.txt.tar.gz'
2026-06-05 07:13:30 INFO:	Decompressing file '/busco_wd/busco_downloads/placement_files/tree_metadata.bacteria_odb12.2.2026-05-27.txt.tar.gz'
2026-06-05 07:13:30 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.bacteria_odb12.2.2026-05-27.faa.tar.gz'
2026-06-05 07:13:32 INFO:	Decompressing file '/busco_wd/busco_downloads/placement_files/supermatrix.aln.bacteria_odb12.2.2026-05-27.faa.tar.gz'
2026-06-05 07:13:33 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb12.2.2026-05-27.txt.tar.gz'
2026-06-05 07:13:33 INFO:	Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb12.2.2026-05-27.txt.tar.gz'
2026-06-05 07:13:33 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.bacteria_odb12.2.2026-05-27.txt.tar.gz'
2026-06-05 07:13:34 INFO:	Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxid-lineage.bacteria_odb12.2.2026-05-27.txt.tar.gz'
2026-06-05 07:13:34 INFO:	Extract markers...
2026-06-05 07:13:34 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/list_of_reference_markers.bacteria_odb12.2.2026-05-27.txt is the last available version.
2026-06-05 07:13:34 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/tree.bacteria_odb12.2.2026-05-27.nwk is the last available version.
2026-06-05 07:13:34 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/tree_metadata.bacteria_odb12.2.2026-05-27.txt is the last available version.
2026-06-05 07:13:34 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/supermatrix.aln.bacteria_odb12.2.2026-05-27.faa is the last available version.
2026-06-05 07:13:34 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb12.2.2026-05-27.txt is the last available version.
2026-06-05 07:13:34 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/mapping_taxid-lineage.bacteria_odb12.2.2026-05-27.txt is the last available version.
2026-06-05 07:13:34 INFO:	Place the markers on the reference tree...
2026-06-05 07:13:34 INFO:	Running 1 job(s) on sepp, starting at 06/05/2026 07:13:34
2026-06-05 07:14:22 INFO:	[sepp]	1 of 1 task(s) completed
2026-06-05 07:14:23 INFO:	Not enough markers were placed on the tree (11). Root lineage bacteria is kept
2026-06-05 07:14:23 INFO:	The local file or folder /busco_wd/busco_downloads/lineages/bacteria_odb12.2 is the last available version.
2026-06-05 07:14:23 INFO:	

    ---------------------------------------------------
    |Results from dataset bacteria_odb12.2             |
    ---------------------------------------------------
    |C:20.7%[S:20.7%,D:0.0%],F:1.7%,M:77.6%,n:116      |
    |24    Complete BUSCOs (C)                         |
    |24    Complete and single-copy BUSCOs (S)         |
    |0    Complete and duplicated BUSCOs (D)           |
    |2    Fragmented BUSCOs (F)                        |
    |90    Missing BUSCOs (M)                          |
    |116    Total BUSCO groups searched                |
    ---------------------------------------------------
2026-06-05 07:14:23 INFO:	BUSCO analysis done with WARNING(s). Total running time: 180 seconds

***** Summary of warnings: *****
2026-06-05 07:14:23 WARNING:	2026-06-05 07:11:22 WARNING:busco.BuscoConfig	Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.
2026-06-05 07:14:23 WARNING:	2026-06-05 07:13:29 WARNING:busco.busco_tools.hmmer	1 of 2 Complete matches (50.0%) contain internal stop codons in Miniprot gene predictions
2026-06-05 07:14:23 WARNING:	2026-06-05 07:13:29 WARNING:busco.busco_tools.hmmer	BUSCO gene predictions from Miniprot have low average identity (0.29). You may want to repeat the analysis using the Metaeuk pipeline.
2026-06-05 07:14:23 INFO:	Results written in /busco_wd/test_bacteria
2026-06-05 07:14:23 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2026-06-05 07:14:23 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
2026-06-05 07:14:23 INFO:	Thank you for using BUSCO! Anonymous usage data is gathered to improve the tool. You may opt out with --opt-out-run-stats.
