2023-04-28 14:24:43 INFO:	***** Start a BUSCO v5.4.7 analysis, current time: 04/28/2023 14:24:43 *****
2023-04-28 14:24:43 INFO:	Configuring BUSCO with local environment
2023-04-28 14:24:43 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.
2023-04-28 14:24:43 INFO:	Mode is genome
2023-04-28 14:24:43 INFO:	'Force' option selected; overwriting previous results directory
2023-04-28 14:24:44 INFO:	Downloading information on latest versions of BUSCO data...
2023-04-28 14:24:46 INFO:	Input file is /busco_wd/test_data/bacteria/genome.fna
2023-04-28 14:24:46 INFO:	No lineage specified. Running lineage auto selector.

2023-04-28 14:24:46 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.
2023-04-28 14:24:46 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2023-04-28 14:24:46 INFO:	Running 1 job(s) on bbtools, starting at 04/28/2023 14:24:46
2023-04-28 14:24:48 INFO:	[bbtools]	1 of 1 task(s) completed
2023-04-28 14:24:48 INFO:	***** Run Prodigal on input to predict and extract genes *****
2023-04-28 14:24:48 INFO:	Running Prodigal with genetic code 11 in single mode
2023-04-28 14:24:48 INFO:	Running 1 job(s) on prodigal, starting at 04/28/2023 14:24:48
2023-04-28 14:24:50 INFO:	[prodigal]	1 of 1 task(s) completed
2023-04-28 14:24:50 INFO:	Genetic code 11 selected as optimal
2023-04-28 14:24:50 INFO:	***** Run HMMER on gene sequences *****
2023-04-28 14:24:50 INFO:	Running 194 job(s) on hmmsearch, starting at 04/28/2023 14:24:50
2023-04-28 14:24:51 INFO:	[hmmsearch]	20 of 194 task(s) completed
2023-04-28 14:24:52 INFO:	[hmmsearch]	39 of 194 task(s) completed
2023-04-28 14:24:52 INFO:	[hmmsearch]	59 of 194 task(s) completed
2023-04-28 14:24:52 INFO:	[hmmsearch]	78 of 194 task(s) completed
2023-04-28 14:24:52 INFO:	[hmmsearch]	97 of 194 task(s) completed
2023-04-28 14:24:52 INFO:	[hmmsearch]	117 of 194 task(s) completed
2023-04-28 14:24:52 INFO:	[hmmsearch]	136 of 194 task(s) completed
2023-04-28 14:24:52 INFO:	[hmmsearch]	156 of 194 task(s) completed
2023-04-28 14:24:53 INFO:	[hmmsearch]	175 of 194 task(s) completed
2023-04-28 14:24:53 INFO:	[hmmsearch]	194 of 194 task(s) completed
2023-04-28 14:24:54 INFO:	Results:	C:5.2%[S:5.2%,D:0.0%],F:1.5%,M:93.3%,n:194	   

2023-04-28 14:24:55 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2023-04-28 14:24:55 INFO:	Running 1 job(s) on bbtools, starting at 04/28/2023 14:24:55
2023-04-28 14:24:57 INFO:	[bbtools]	1 of 1 task(s) completed
2023-04-28 14:24:57 INFO:	***** Run Prodigal on input to predict and extract genes *****
2023-04-28 14:24:58 INFO:	Genetic code 11 selected as optimal
2023-04-28 14:24:58 INFO:	***** Run HMMER on gene sequences *****
2023-04-28 14:24:58 INFO:	Running 124 job(s) on hmmsearch, starting at 04/28/2023 14:24:58
2023-04-28 14:24:59 INFO:	[hmmsearch]	13 of 124 task(s) completed
2023-04-28 14:25:00 INFO:	[hmmsearch]	25 of 124 task(s) completed
2023-04-28 14:25:00 INFO:	[hmmsearch]	38 of 124 task(s) completed
2023-04-28 14:25:00 INFO:	[hmmsearch]	50 of 124 task(s) completed
2023-04-28 14:25:00 INFO:	[hmmsearch]	63 of 124 task(s) completed
2023-04-28 14:25:00 INFO:	[hmmsearch]	75 of 124 task(s) completed
2023-04-28 14:25:00 INFO:	[hmmsearch]	87 of 124 task(s) completed
2023-04-28 14:25:00 INFO:	[hmmsearch]	100 of 124 task(s) completed
2023-04-28 14:25:01 INFO:	[hmmsearch]	112 of 124 task(s) completed
2023-04-28 14:25:01 INFO:	[hmmsearch]	124 of 124 task(s) completed
2023-04-28 14:25:03 INFO:	Results:	C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124	   

2023-04-28 14:25:03 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2023-04-28 14:25:03 INFO:	Running 1 job(s) on bbtools, starting at 04/28/2023 14:25:03
2023-04-28 14:25:06 INFO:	[bbtools]	1 of 1 task(s) completed
2023-04-28 14:25:06 INFO:	Running 1 job(s) on metaeuk, starting at 04/28/2023 14:25:06
2023-04-28 14:25:49 INFO:	[metaeuk]	1 of 1 task(s) completed
2023-04-28 14:25:50 INFO:	***** Run HMMER on gene sequences *****
2023-04-28 14:25:50 INFO:	Running 255 job(s) on hmmsearch, starting at 04/28/2023 14:25:50
2023-04-28 14:25:52 INFO:	[hmmsearch]	26 of 255 task(s) completed
2023-04-28 14:25:52 INFO:	[hmmsearch]	51 of 255 task(s) completed
2023-04-28 14:25:52 INFO:	[hmmsearch]	77 of 255 task(s) completed
2023-04-28 14:25:52 INFO:	[hmmsearch]	102 of 255 task(s) completed
2023-04-28 14:25:52 INFO:	[hmmsearch]	128 of 255 task(s) completed
2023-04-28 14:25:52 INFO:	[hmmsearch]	153 of 255 task(s) completed
2023-04-28 14:25:52 INFO:	[hmmsearch]	179 of 255 task(s) completed
2023-04-28 14:25:53 INFO:	[hmmsearch]	204 of 255 task(s) completed
2023-04-28 14:25:53 INFO:	[hmmsearch]	230 of 255 task(s) completed
2023-04-28 14:25:53 INFO:	[hmmsearch]	255 of 255 task(s) completed
2023-04-28 14:25:55 INFO:	Validating exons and removing overlapping matches
2023-04-28 14:25:55 INFO:	0 candidate overlapping regions found
2023-04-28 14:25:55 INFO:	3 exons in total
2023-04-28 14:25:55 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2023-04-28 14:25:55 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2023-04-28 14:26:13 INFO:	Running 1 job(s) on metaeuk, starting at 04/28/2023 14:26:13
2023-04-28 14:27:12 INFO:	[metaeuk]	1 of 1 task(s) completed
2023-04-28 14:27:13 INFO:	***** Run HMMER on gene sequences *****
2023-04-28 14:27:13 INFO:	Running 252 job(s) on hmmsearch, starting at 04/28/2023 14:27:13
2023-04-28 14:27:15 INFO:	[hmmsearch]	26 of 252 task(s) completed
2023-04-28 14:27:15 INFO:	[hmmsearch]	51 of 252 task(s) completed
2023-04-28 14:27:15 INFO:	[hmmsearch]	76 of 252 task(s) completed
2023-04-28 14:27:15 INFO:	[hmmsearch]	101 of 252 task(s) completed
2023-04-28 14:27:15 INFO:	[hmmsearch]	126 of 252 task(s) completed
2023-04-28 14:27:15 INFO:	[hmmsearch]	152 of 252 task(s) completed
2023-04-28 14:27:15 INFO:	[hmmsearch]	177 of 252 task(s) completed
2023-04-28 14:27:16 INFO:	[hmmsearch]	202 of 252 task(s) completed
2023-04-28 14:27:16 INFO:	[hmmsearch]	202 of 252 task(s) completed
2023-04-28 14:27:16 INFO:	[hmmsearch]	227 of 252 task(s) completed
2023-04-28 14:27:16 INFO:	[hmmsearch]	252 of 252 task(s) completed
2023-04-28 14:27:17 INFO:	Validating exons and removing overlapping matches
2023-04-28 14:27:18 INFO:	0 candidate overlapping regions found
2023-04-28 14:27:18 INFO:	3 exons in total
2023-04-28 14:27:18 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2023-04-28 14:27:18 INFO:	bacteria_odb10 selected

2023-04-28 14:27:18 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2023-04-28 14:27:18 INFO:	Extract markers...
2023-04-28 14:27:18 INFO:	Place the markers on the reference tree...
2023-04-28 14:27:18 INFO:	Running 1 job(s) on sepp, starting at 04/28/2023 14:27:18
2023-04-28 14:28:48 INFO:	[sepp]	1 of 1 task(s) completed
2023-04-28 14:28:48 INFO:	Not enough markers were placed on the tree (11). Root lineage bacteria is kept
2023-04-28 14:28:48 INFO:	

	--------------------------------------------------
	|Results from dataset bacteria_odb10              |
	--------------------------------------------------
	|C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124     |
	|26	Complete BUSCOs (C)                       |
	|26	Complete and single-copy BUSCOs (S)       |
	|0	Complete and duplicated BUSCOs (D)        |
	|1	Fragmented BUSCOs (F)                     |
	|97	Missing BUSCOs (M)                        |
	|124	Total BUSCO groups searched               |
	--------------------------------------------------
2023-04-28 14:28:48 INFO:	BUSCO analysis done with WARNING(s). Total running time: 243 seconds

***** Summary of warnings: *****
2023-04-28 14:24:43 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.

2023-04-28 14:28:48 INFO:	Results written in /busco_wd/test_bacteria
2023-04-28 14:28:48 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2023-04-28 14:28:48 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
