2025-07-09 08:53:26 INFO:	***** Start a BUSCO v6.0.0 analysis, current time: 07/09/2025 08:53:26 *****
2025-07-09 08:53:26 INFO:	Configuring BUSCO with local environment
2025-07-09 08:53:26 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.
2025-07-09 08:53:26 INFO:	Running genome mode
2025-07-09 08:53:26 INFO:	'Force' option selected; overwriting previous results directory
2025-07-09 08:53:26 INFO:	Downloading information on latest versions of BUSCO data...
2025-07-09 08:53:28 INFO:	Input file is /busco_wd/test_data/bacteria/genome.fna
2025-07-09 08:53:28 INFO:	No lineage specified. Running lineage auto selector.

2025-07-09 08:53:28 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.
2025-07-09 08:53:28 INFO:	Renaming /busco_wd/busco_downloads/lineages/archaea_odb12 into /busco_wd/busco_downloads/lineages/archaea_odb12.old
2025-07-09 08:53:28 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/archaea_odb12.2025-05-14.tar.gz'
2025-07-09 08:53:29 INFO:	Decompressing file '/busco_wd/busco_downloads/lineages/archaea_odb12.tar.gz'
2025-07-09 08:53:30 WARNING:	The file or folder archaea_odb12 was updated automatically.
2025-07-09 08:53:30 INFO:	Running BUSCO using lineage dataset archaea_odb12 (prokaryota, 2025-05-14)
2025-07-09 08:53:30 INFO:	Running 1 job(s) on bbtools, starting at 07/09/2025 08:53:30
2025-07-09 08:53:31 INFO:	[bbtools]	1 of 1 task(s) completed
2025-07-09 08:53:31 INFO:	***** Run Prodigal on input to predict and extract genes *****
2025-07-09 08:53:31 INFO:	Running Prodigal with genetic code 11 in single mode
2025-07-09 08:53:31 INFO:	Running 1 job(s) on prodigal, starting at 07/09/2025 08:53:31
2025-07-09 08:53:33 INFO:	[prodigal]	1 of 1 task(s) completed
2025-07-09 08:53:33 INFO:	Genetic code 11 selected as optimal
2025-07-09 08:53:33 INFO:	***** Run HMMER on gene sequences *****
2025-07-09 08:53:33 INFO:	Running 195 job(s) on hmmsearch, starting at 07/09/2025 08:53:33
2025-07-09 08:53:34 INFO:	[hmmsearch]	20 of 195 task(s) completed
2025-07-09 08:53:34 INFO:	[hmmsearch]	39 of 195 task(s) completed
2025-07-09 08:53:34 INFO:	[hmmsearch]	59 of 195 task(s) completed
2025-07-09 08:53:34 INFO:	[hmmsearch]	78 of 195 task(s) completed
2025-07-09 08:53:34 INFO:	[hmmsearch]	98 of 195 task(s) completed
2025-07-09 08:53:34 INFO:	[hmmsearch]	117 of 195 task(s) completed
2025-07-09 08:53:34 INFO:	[hmmsearch]	137 of 195 task(s) completed
2025-07-09 08:53:34 INFO:	[hmmsearch]	156 of 195 task(s) completed
2025-07-09 08:53:34 INFO:	[hmmsearch]	176 of 195 task(s) completed
2025-07-09 08:53:34 INFO:	[hmmsearch]	195 of 195 task(s) completed
2025-07-09 08:53:34 INFO:	Results:	C:4.6%[S:4.6%,D:0.0%],F:1.0%,M:94.4%,n:195	   

2025-07-09 08:53:34 INFO:	Renaming /busco_wd/busco_downloads/lineages/bacteria_odb12 into /busco_wd/busco_downloads/lineages/bacteria_odb12.old
2025-07-09 08:53:34 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb12.2025-05-14.tar.gz'
2025-07-09 08:53:35 INFO:	Decompressing file '/busco_wd/busco_downloads/lineages/bacteria_odb12.tar.gz'
2025-07-09 08:53:36 WARNING:	The file or folder bacteria_odb12 was updated automatically.
2025-07-09 08:53:36 INFO:	Running BUSCO using lineage dataset bacteria_odb12 (prokaryota, 2025-05-14)
2025-07-09 08:53:36 INFO:	Skipping BBTools as already run
2025-07-09 08:53:36 INFO:	***** Run Prodigal on input to predict and extract genes *****
2025-07-09 08:53:36 INFO:	Genetic code 11 selected as optimal
2025-07-09 08:53:36 INFO:	***** Run HMMER on gene sequences *****
2025-07-09 08:53:36 INFO:	Running 116 job(s) on hmmsearch, starting at 07/09/2025 08:53:36
2025-07-09 08:53:37 INFO:	[hmmsearch]	12 of 116 task(s) completed
2025-07-09 08:53:37 INFO:	[hmmsearch]	24 of 116 task(s) completed
2025-07-09 08:53:37 INFO:	[hmmsearch]	35 of 116 task(s) completed
2025-07-09 08:53:37 INFO:	[hmmsearch]	47 of 116 task(s) completed
2025-07-09 08:53:37 INFO:	[hmmsearch]	58 of 116 task(s) completed
2025-07-09 08:53:37 INFO:	[hmmsearch]	70 of 116 task(s) completed
2025-07-09 08:53:37 INFO:	[hmmsearch]	82 of 116 task(s) completed
2025-07-09 08:53:37 INFO:	[hmmsearch]	93 of 116 task(s) completed
2025-07-09 08:53:37 INFO:	[hmmsearch]	105 of 116 task(s) completed
2025-07-09 08:53:37 INFO:	[hmmsearch]	116 of 116 task(s) completed
2025-07-09 08:53:37 INFO:	Results:	C:20.7%[S:20.7%,D:0.0%],F:1.7%,M:77.6%,n:116	   

2025-07-09 08:53:37 INFO:	Renaming /busco_wd/busco_downloads/lineages/eukaryota_odb12 into /busco_wd/busco_downloads/lineages/eukaryota_odb12.old
2025-07-09 08:53:37 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb12.2025-07-01.tar.gz'
2025-07-09 08:53:38 INFO:	Decompressing file '/busco_wd/busco_downloads/lineages/eukaryota_odb12.tar.gz'
2025-07-09 08:53:38 WARNING:	The file or folder eukaryota_odb12 was updated automatically.
2025-07-09 08:53:39 INFO:	Running BUSCO using lineage dataset eukaryota_odb12 (eukaryota, 2025-07-01)
2025-07-09 08:53:39 INFO:	Skipping BBTools as already run
2025-07-09 08:53:39 INFO:	Running 1 job(s) on miniprot_index, starting at 07/09/2025 08:53:39
2025-07-09 08:53:39 INFO:	[miniprot_index]	1 of 1 task(s) completed
2025-07-09 08:53:40 INFO:	Running 1 job(s) on miniprot_align, starting at 07/09/2025 08:53:40
2025-07-09 08:53:51 INFO:	[miniprot_align]	1 of 1 task(s) completed
2025-07-09 08:53:52 INFO:	***** Run HMMER on gene sequences *****
2025-07-09 08:53:52 INFO:	Running 37 job(s) on hmmsearch, starting at 07/09/2025 08:53:52
2025-07-09 08:53:52 INFO:	[hmmsearch]	4 of 37 task(s) completed
2025-07-09 08:53:52 INFO:	[hmmsearch]	8 of 37 task(s) completed
2025-07-09 08:53:52 INFO:	[hmmsearch]	12 of 37 task(s) completed
2025-07-09 08:53:52 INFO:	[hmmsearch]	15 of 37 task(s) completed
2025-07-09 08:53:52 INFO:	[hmmsearch]	19 of 37 task(s) completed
2025-07-09 08:53:52 INFO:	[hmmsearch]	23 of 37 task(s) completed
2025-07-09 08:53:52 INFO:	[hmmsearch]	26 of 37 task(s) completed
2025-07-09 08:53:52 INFO:	[hmmsearch]	30 of 37 task(s) completed
2025-07-09 08:53:52 INFO:	[hmmsearch]	34 of 37 task(s) completed
2025-07-09 08:53:52 INFO:	[hmmsearch]	37 of 37 task(s) completed
2025-07-09 08:53:52 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2025-07-09 08:53:52 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:129	   

2025-07-09 08:53:52 INFO:	bacteria_odb12 selected

2025-07-09 08:53:52 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2025-07-09 08:53:53 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/list_of_reference_markers.bacteria_odb12.2024-11-15.txt is the last available version.
2025-07-09 08:53:53 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/tree.bacteria_odb12.2024-11-15.nwk is the last available version.
2025-07-09 08:53:53 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/tree_metadata.bacteria_odb12.2024-11-15.txt is the last available version.
2025-07-09 08:53:53 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/supermatrix.aln.bacteria_odb12.2024-11-15.faa is the last available version.
2025-07-09 08:53:53 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb12.2024-11-15.txt is the last available version.
2025-07-09 08:53:53 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/mapping_taxid-lineage.bacteria_odb12.2024-11-15.txt is the last available version.
2025-07-09 08:53:53 INFO:	Extract markers...
2025-07-09 08:53:53 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/list_of_reference_markers.bacteria_odb12.2024-11-15.txt is the last available version.
2025-07-09 08:53:53 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/tree.bacteria_odb12.2024-11-15.nwk is the last available version.
2025-07-09 08:53:53 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/tree_metadata.bacteria_odb12.2024-11-15.txt is the last available version.
2025-07-09 08:53:53 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/supermatrix.aln.bacteria_odb12.2024-11-15.faa is the last available version.
2025-07-09 08:53:53 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb12.2024-11-15.txt is the last available version.
2025-07-09 08:53:53 INFO:	The local file or folder /busco_wd/busco_downloads/placement_files/mapping_taxid-lineage.bacteria_odb12.2024-11-15.txt is the last available version.
2025-07-09 08:53:53 INFO:	Place the markers on the reference tree...
2025-07-09 08:53:53 INFO:	Running 1 job(s) on sepp, starting at 07/09/2025 08:53:53
2025-07-09 08:54:41 INFO:	[sepp]	1 of 1 task(s) completed
2025-07-09 08:54:41 INFO:	Not enough markers were placed on the tree (11). Root lineage bacteria is kept
2025-07-09 08:54:41 INFO:	The local file or folder /busco_wd/busco_downloads/lineages/bacteria_odb12 is the last available version.
2025-07-09 08:54:41 INFO:	

    ---------------------------------------------------
    |Results from dataset bacteria_odb12               |
    ---------------------------------------------------
    |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                |
    ---------------------------------------------------
2025-07-09 08:54:41 INFO:	BUSCO analysis done with WARNING(s). Total running time: 73 seconds

***** Summary of warnings: *****
2025-07-09 08:53:26 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.
2025-07-09 08:53:30 WARNING:busco.BuscoDownloadManager	The file or folder archaea_odb12 was updated automatically.
2025-07-09 08:53:36 WARNING:busco.BuscoDownloadManager	The file or folder bacteria_odb12 was updated automatically.
2025-07-09 08:53:38 WARNING:busco.BuscoDownloadManager	The file or folder eukaryota_odb12 was updated automatically.
2025-07-09 08:53:52 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.

2025-07-09 08:54:41 INFO:	Results written in /busco_wd/test_bacteria
2025-07-09 08:54:41 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-07-09 08:54:41 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
2025-07-09 08:54:41 INFO:	Thank you for using BUSCO! Anonymous usage data is gathered to improve the tool. You may opt out with --opt-out-run-stats.
