INFO:	***** Start a BUSCO v4.1.2 analysis, current time: 07/01/2020 18:43:08 *****
INFO:	Configuring BUSCO with /busco/config/config.ini
INFO:	Mode is genome
INFO:	Input file is genome.fna
INFO:	Downloading information on latest versions of BUSCO data...
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.
INFO:	No lineage specified. Running lineage auto selector.

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.
INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/archaea_odb10.2019-01-04.tar.gz'
INFO:	Decompressing file '/busco_wd/busco_downloads/lineages/archaea_odb10.tar.gz'
INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2019-01-04)
INFO:	***** Run Prodigal on input to predict and extract genes *****
INFO:	Running Prodigal with genetic code 11 in single mode
INFO:	Running 1 job(s) on prodigal, starting at 07/01/2020 18:43:09
INFO:	[prodigal]	1 of 1 task(s) completed
INFO:	Genetic code 11 selected as optimal
INFO:	***** Run HMMER on gene sequences *****
INFO:	Running 194 job(s) on hmmsearch, starting at 07/01/2020 18:43:10
INFO:	[hmmsearch]	20 of 194 task(s) completed
INFO:	[hmmsearch]	39 of 194 task(s) completed
INFO:	[hmmsearch]	59 of 194 task(s) completed
INFO:	[hmmsearch]	78 of 194 task(s) completed
INFO:	[hmmsearch]	97 of 194 task(s) completed
INFO:	[hmmsearch]	117 of 194 task(s) completed
INFO:	[hmmsearch]	136 of 194 task(s) completed
INFO:	[hmmsearch]	156 of 194 task(s) completed
INFO:	[hmmsearch]	175 of 194 task(s) completed
INFO:	[hmmsearch]	194 of 194 task(s) completed
INFO:	Results:	C:5.2%[S:5.2%,D:0.0%],F:1.5%,M:93.3%,n:194	   

INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/bacteria_odb10.2019-06-26.tar.gz'
INFO:	Decompressing file '/busco_wd/busco_downloads/lineages/bacteria_odb10.tar.gz'
INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2019-06-26)
INFO:	***** Run Prodigal on input to predict and extract genes *****
INFO:	Genetic code 11 selected as optimal
INFO:	***** Run HMMER on gene sequences *****
INFO:	Running 124 job(s) on hmmsearch, starting at 07/01/2020 18:43:13
INFO:	[hmmsearch]	13 of 124 task(s) completed
INFO:	[hmmsearch]	25 of 124 task(s) completed
INFO:	[hmmsearch]	38 of 124 task(s) completed
INFO:	[hmmsearch]	50 of 124 task(s) completed
INFO:	[hmmsearch]	63 of 124 task(s) completed
INFO:	[hmmsearch]	75 of 124 task(s) completed
INFO:	[hmmsearch]	87 of 124 task(s) completed
INFO:	[hmmsearch]	100 of 124 task(s) completed
INFO:	[hmmsearch]	112 of 124 task(s) completed
INFO:	[hmmsearch]	124 of 124 task(s) completed
INFO:	Results:	C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124	   

INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/eukaryota_odb10.2019-11-20.tar.gz'
INFO:	Decompressing file '/busco_wd/busco_downloads/lineages/eukaryota_odb10.tar.gz'
INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2019-11-20)
INFO:	Running 1 job(s) on makeblastdb, starting at 07/01/2020 18:43:16
INFO:	Creating BLAST database with input file
INFO:	[makeblastdb]	1 of 1 task(s) completed
INFO:	Running a BLAST search for BUSCOs against created database
INFO:	Running 1 job(s) on tblastn, starting at 07/01/2020 18:43:16
INFO:	[tblastn]	1 of 1 task(s) completed
INFO:	Running Augustus gene predictor on BLAST search results.
INFO:	Running Augustus prediction using fly as species:
INFO:	Running 10 job(s) on augustus, starting at 07/01/2020 18:43:18
INFO:	[augustus]	1 of 10 task(s) completed
INFO:	[augustus]	2 of 10 task(s) completed
INFO:	[augustus]	3 of 10 task(s) completed
INFO:	[augustus]	4 of 10 task(s) completed
INFO:	[augustus]	5 of 10 task(s) completed
INFO:	[augustus]	6 of 10 task(s) completed
INFO:	[augustus]	7 of 10 task(s) completed
INFO:	[augustus]	8 of 10 task(s) completed
INFO:	[augustus]	9 of 10 task(s) completed
INFO:	[augustus]	10 of 10 task(s) completed
INFO:	Extracting predicted proteins...
INFO:	***** Run HMMER on gene sequences *****
INFO:	Running 4 job(s) on hmmsearch, starting at 07/01/2020 18:43:51
INFO:	[hmmsearch]	1 of 4 task(s) completed
INFO:	[hmmsearch]	2 of 4 task(s) completed
INFO:	[hmmsearch]	3 of 4 task(s) completed
INFO:	[hmmsearch]	4 of 4 task(s) completed
WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:255	   

INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
INFO:	Running a BLAST search for BUSCOs against created database
INFO:	Running 1 job(s) on tblastn, starting at 07/01/2020 18:43:52
INFO:	[tblastn]	1 of 1 task(s) completed
INFO:	Converting predicted genes to short genbank files
WARNING:	No jobs to run on gff2gbSmallDNA.pl
INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
INFO:	Running 1 job(s) on new_species.pl, starting at 07/01/2020 18:44:07
INFO:	[new_species.pl]	1 of 1 task(s) completed
INFO:	Running 1 job(s) on etraining, starting at 07/01/2020 18:44:08
INFO:	[etraining]	1 of 1 task(s) completed
INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 255
INFO:	Running Augustus gene predictor on BLAST search results.
INFO:	Running Augustus prediction using BUSCO_test_bacteria as species:
INFO:	Running 14 job(s) on augustus, starting at 07/01/2020 18:44:08
INFO:	[augustus]	2 of 14 task(s) completed
INFO:	[augustus]	3 of 14 task(s) completed
INFO:	[augustus]	5 of 14 task(s) completed
INFO:	[augustus]	6 of 14 task(s) completed
INFO:	[augustus]	7 of 14 task(s) completed
INFO:	[augustus]	9 of 14 task(s) completed
INFO:	[augustus]	10 of 14 task(s) completed
INFO:	[augustus]	12 of 14 task(s) completed
INFO:	[augustus]	13 of 14 task(s) completed
INFO:	[augustus]	14 of 14 task(s) completed
INFO:	Extracting predicted proteins...
INFO:	***** Run HMMER on gene sequences *****
WARNING:	No jobs to run on hmmsearch
WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:255	   

WARNING:	Augustus did not produce a retrained species folder.
INFO:	bacteria_odb10 selected

INFO:	***** Searching tree for chosen lineage to find best taxonomic match *****

INFO:	Extract markers...
INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/placement_files/list_of_reference_markers.bacteria_odb10.2019-12-16.txt.tar.gz'
INFO:	Decompressing file '/busco_wd/busco_downloads/placement_files/list_of_reference_markers.bacteria_odb10.2019-12-16.txt.tar.gz'
INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/placement_files/tree.bacteria_odb10.2019-12-16.nwk.tar.gz'
INFO:	Decompressing file '/busco_wd/busco_downloads/placement_files/tree.bacteria_odb10.2019-12-16.nwk.tar.gz'
INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/placement_files/tree_metadata.bacteria_odb10.2019-12-16.txt.tar.gz'
INFO:	Decompressing file '/busco_wd/busco_downloads/placement_files/tree_metadata.bacteria_odb10.2019-12-16.txt.tar.gz'
INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/placement_files/supermatrix.aln.bacteria_odb10.2019-12-16.faa.tar.gz'
INFO:	Decompressing file '/busco_wd/busco_downloads/placement_files/supermatrix.aln.bacteria_odb10.2019-12-16.faa.tar.gz'
INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb10.2019-12-16.txt.tar.gz'
INFO:	Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.bacteria_odb10.2019-12-16.txt.tar.gz'
INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/placement_files/mapping_taxid-lineage.bacteria_odb10.2019-12-16.txt.tar.gz'
INFO:	Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxid-lineage.bacteria_odb10.2019-12-16.txt.tar.gz'
INFO:	Place the markers on the reference tree...
INFO:	Running 1 job(s) on sepp, starting at 07/01/2020 18:44:10
INFO:	[sepp]	1 of 1 task(s) completed
INFO:	Not enough markers were placed on the tree (11). Root lineage bacteria is kept
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               |
	--------------------------------------------------
INFO:	BUSCO analysis done with WARNING(s). Total running time: 127 seconds

***** Summary of warnings: *****
WARNING:busco.ConfigManager	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.
WARNING:busco.BuscoTools	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
WARNING:busco.Toolset	No jobs to run on gff2gbSmallDNA.pl
WARNING:busco.Toolset	No jobs to run on hmmsearch
WARNING:busco.BuscoTools	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
WARNING:busco.BuscoTools	Augustus did not produce a retrained species folder.

INFO:	Results written in /busco_wd/test_bacteria

