2022-12-05 16:29:58 INFO:	***** Start a BUSCO v5.4.4 analysis, current time: 12/05/2022 16:29:58 *****
2022-12-05 16:29:58 INFO:	Configuring BUSCO with local environment
2022-12-05 16:29:58 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.
2022-12-05 16:29:58 INFO:	Mode is genome
2022-12-05 16:29:58 INFO:	Downloading information on latest versions of BUSCO data...
2022-12-05 16:30:00 INFO:	Input file is /busco_wd/test_data/bacteria/genome.fna
2022-12-05 16:30:00 INFO:	No lineage specified. Running lineage auto selector.

2022-12-05 16:30:00 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.
2022-12-05 16:30:00 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2022-12-05 16:30:00 INFO:	Running 1 job(s) on bbtools, starting at 12/05/2022 16:30:00
2022-12-05 16:30:02 INFO:	[bbtools]	1 of 1 task(s) completed
2022-12-05 16:30:02 INFO:	***** Run Prodigal on input to predict and extract genes *****
2022-12-05 16:30:02 INFO:	Running Prodigal with genetic code 11 in single mode
2022-12-05 16:30:02 INFO:	Running 1 job(s) on prodigal, starting at 12/05/2022 16:30:02
2022-12-05 16:30:04 INFO:	[prodigal]	1 of 1 task(s) completed
2022-12-05 16:30:04 INFO:	Genetic code 11 selected as optimal
2022-12-05 16:30:04 INFO:	***** Run HMMER on gene sequences *****
2022-12-05 16:30:04 INFO:	Running 194 job(s) on hmmsearch, starting at 12/05/2022 16:30:04
2022-12-05 16:30:06 INFO:	[hmmsearch]	20 of 194 task(s) completed
2022-12-05 16:30:06 INFO:	[hmmsearch]	39 of 194 task(s) completed
2022-12-05 16:30:06 INFO:	[hmmsearch]	59 of 194 task(s) completed
2022-12-05 16:30:06 INFO:	[hmmsearch]	78 of 194 task(s) completed
2022-12-05 16:30:06 INFO:	[hmmsearch]	97 of 194 task(s) completed
2022-12-05 16:30:07 INFO:	[hmmsearch]	117 of 194 task(s) completed
2022-12-05 16:30:07 INFO:	[hmmsearch]	136 of 194 task(s) completed
2022-12-05 16:30:07 INFO:	[hmmsearch]	156 of 194 task(s) completed
2022-12-05 16:30:07 INFO:	[hmmsearch]	175 of 194 task(s) completed
2022-12-05 16:30:07 INFO:	[hmmsearch]	194 of 194 task(s) completed
2022-12-05 16:30:09 INFO:	Results:	C:5.2%[S:5.2%,D:0.0%],F:1.5%,M:93.3%,n:194	   

2022-12-05 16:30:09 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2022-12-05 16:30:09 INFO:	Running 1 job(s) on bbtools, starting at 12/05/2022 16:30:09
2022-12-05 16:30:11 INFO:	[bbtools]	1 of 1 task(s) completed
2022-12-05 16:30:11 INFO:	***** Run Prodigal on input to predict and extract genes *****
2022-12-05 16:30:11 INFO:	Genetic code 11 selected as optimal
2022-12-05 16:30:11 INFO:	***** Run HMMER on gene sequences *****
2022-12-05 16:30:11 INFO:	Running 124 job(s) on hmmsearch, starting at 12/05/2022 16:30:11
2022-12-05 16:30:12 INFO:	[hmmsearch]	13 of 124 task(s) completed
2022-12-05 16:30:13 INFO:	[hmmsearch]	25 of 124 task(s) completed
2022-12-05 16:30:13 INFO:	[hmmsearch]	38 of 124 task(s) completed
2022-12-05 16:30:13 INFO:	[hmmsearch]	50 of 124 task(s) completed
2022-12-05 16:30:13 INFO:	[hmmsearch]	63 of 124 task(s) completed
2022-12-05 16:30:13 INFO:	[hmmsearch]	75 of 124 task(s) completed
2022-12-05 16:30:13 INFO:	[hmmsearch]	87 of 124 task(s) completed
2022-12-05 16:30:13 INFO:	[hmmsearch]	100 of 124 task(s) completed
2022-12-05 16:30:14 INFO:	[hmmsearch]	112 of 124 task(s) completed
2022-12-05 16:30:14 INFO:	[hmmsearch]	124 of 124 task(s) completed
2022-12-05 16:30:16 INFO:	Results:	C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124	   

2022-12-05 16:30:17 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2022-12-05 16:30:17 INFO:	Running 1 job(s) on bbtools, starting at 12/05/2022 16:30:17
2022-12-05 16:30:19 INFO:	[bbtools]	1 of 1 task(s) completed
2022-12-05 16:30:19 INFO:	Running 1 job(s) on metaeuk, starting at 12/05/2022 16:30:19
2022-12-05 16:31:01 INFO:	[metaeuk]	1 of 1 task(s) completed
2022-12-05 16:31:02 INFO:	***** Run HMMER on gene sequences *****
2022-12-05 16:31:02 INFO:	Running 255 job(s) on hmmsearch, starting at 12/05/2022 16:31:02
2022-12-05 16:31:03 INFO:	[hmmsearch]	26 of 255 task(s) completed
2022-12-05 16:31:04 INFO:	[hmmsearch]	51 of 255 task(s) completed
2022-12-05 16:31:04 INFO:	[hmmsearch]	77 of 255 task(s) completed
2022-12-05 16:31:04 INFO:	[hmmsearch]	102 of 255 task(s) completed
2022-12-05 16:31:05 INFO:	[hmmsearch]	128 of 255 task(s) completed
2022-12-05 16:31:05 INFO:	[hmmsearch]	153 of 255 task(s) completed
2022-12-05 16:31:05 INFO:	[hmmsearch]	179 of 255 task(s) completed
2022-12-05 16:31:05 INFO:	[hmmsearch]	204 of 255 task(s) completed
2022-12-05 16:31:06 INFO:	[hmmsearch]	230 of 255 task(s) completed
2022-12-05 16:31:06 INFO:	[hmmsearch]	255 of 255 task(s) completed
2022-12-05 16:31:08 INFO:	Validating exons and removing overlapping matches
2022-12-05 16:31:10 INFO:	0 candidate overlapping regions found
2022-12-05 16:31:10 INFO:	3 exons in total
2022-12-05 16:31:10 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2022-12-05 16:31:10 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2022-12-05 16:31:26 INFO:	Running 1 job(s) on metaeuk, starting at 12/05/2022 16:31:26
2022-12-05 16:32:23 INFO:	[metaeuk]	1 of 1 task(s) completed
2022-12-05 16:32:24 INFO:	***** Run HMMER on gene sequences *****
2022-12-05 16:32:24 INFO:	Running 252 job(s) on hmmsearch, starting at 12/05/2022 16:32:24
2022-12-05 16:32:26 INFO:	[hmmsearch]	26 of 252 task(s) completed
2022-12-05 16:32:26 INFO:	[hmmsearch]	51 of 252 task(s) completed
2022-12-05 16:32:26 INFO:	[hmmsearch]	76 of 252 task(s) completed
2022-12-05 16:32:26 INFO:	[hmmsearch]	101 of 252 task(s) completed
2022-12-05 16:32:27 INFO:	[hmmsearch]	126 of 252 task(s) completed
2022-12-05 16:32:27 INFO:	[hmmsearch]	152 of 252 task(s) completed
2022-12-05 16:32:27 INFO:	[hmmsearch]	177 of 252 task(s) completed
2022-12-05 16:32:27 INFO:	[hmmsearch]	202 of 252 task(s) completed
2022-12-05 16:32:27 INFO:	[hmmsearch]	227 of 252 task(s) completed
2022-12-05 16:32:27 INFO:	[hmmsearch]	252 of 252 task(s) completed
2022-12-05 16:32:29 INFO:	Validating exons and removing overlapping matches
2022-12-05 16:32:30 INFO:	0 candidate overlapping regions found
2022-12-05 16:32:30 INFO:	3 exons in total
2022-12-05 16:32:30 INFO:	Results:	C:1.2%[S:1.2%,D:0.0%],F:0.0%,M:98.8%,n:255	   

2022-12-05 16:32:30 INFO:	bacteria_odb10 selected

2022-12-05 16:32:30 INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

2022-12-05 16:32:30 INFO:	Extract markers...
2022-12-05 16:32:30 INFO:	Place the markers on the reference tree...
2022-12-05 16:32:30 INFO:	Running 1 job(s) on sepp, starting at 12/05/2022 16:32:30
2022-12-05 16:33:54 INFO:	[sepp]	1 of 1 task(s) completed
2022-12-05 16:33:54 INFO:	Not enough markers were placed on the tree (11). Root lineage bacteria is kept
2022-12-05 16:33:54 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               |
	--------------------------------------------------
2022-12-05 16:33:54 INFO:	BUSCO analysis done with WARNING(s). Total running time: 234 seconds

***** Summary of warnings: *****
2022-12-05 16:29:58 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.

2022-12-05 16:33:54 INFO:	Results written in /busco_wd/test_bacteria
2022-12-05 16:33:54 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2022-12-05 16:33:54 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
