output/quast/Enterococcus/busco_stats/run_spades.log Version 1
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
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output/quast/Enterococcus/busco_stats/run_spades.log
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****************** Start a BUSCO 3.0.2 analysis, current time: 01/23/2021 12:19:13 ****************** Configuration loaded from /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/config.ini Init tools... Check dependencies... Check input file... To reproduce this run: python /home/administrator/conda2/envs/spades/bin/quast.py -i /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/quast_corrected_input/spades.fasta -o spades -l /home/administrator/conda2/envs/spades/lib/python3.6/site-packages/quast_libs/busco/bacteria/ -m genome -c 30 -t /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/tmp/ -sp fly --augustus_parameters '''' Mode is: genome The lineage dataset is: bacteria_odb9 (prokaryota) Delete the current result folder and start a new run Temp directory is /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/tmp/ ****** Phase 1 of 2, initial predictions ****** ****** Step 1/3, current time: 01/23/2021 12:19:13 ****** Create blast database... [makeblastdb] Building a new DB, current time: 01/23/2021 12:19:14 [makeblastdb] New DB name: /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/tmp/spades_3010562973 [makeblastdb] New DB title: /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/quast_corrected_input/spades.fasta [makeblastdb] Sequence type: Nucleotide [makeblastdb] Keep MBits: T [makeblastdb] Maximum file size: 1000000000B [makeblastdb] Adding sequences from FASTA; added 319 sequences in 0.0267169 seconds. [makeblastdb] 1 of 1 task(s) completed at 01/23/2021 12:19:14 Running tblastn, writing output to /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/run_spades/blast_output/tblastn_spades.tsv... [tblastn] 1 of 1 task(s) completed at 01/23/2021 12:19:15 ****** Step 2/3, current time: 01/23/2021 12:19:15 ****** Maximum number of candidate contig per BUSCO limited to: 3 Getting coordinates for candidate regions... Pre-Augustus scaffold extraction... Running Augustus prediction using fly as species: Additional parameters for Augustus are '': [augustus] Please find all logs related to Augustus errors here: /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/run_spades/augustus_output/augustus.log [augustus] 15 of 147 task(s) completed at 01/23/2021 12:19:19 [augustus] 30 of 147 task(s) completed at 01/23/2021 12:19:21 [augustus] 45 of 147 task(s) completed at 01/23/2021 12:19:23 [augustus] 74 of 147 task(s) completed at 01/23/2021 12:19:28 [augustus] 89 of 147 task(s) completed at 01/23/2021 12:19:30 [augustus] 103 of 147 task(s) completed at 01/23/2021 12:19:32 [augustus] 118 of 147 task(s) completed at 01/23/2021 12:19:34 [augustus] 133 of 147 task(s) completed at 01/23/2021 12:19:36 [augustus] 147 of 147 task(s) completed at 01/23/2021 12:19:39 Extracting predicted proteins... ****** Step 3/3, current time: 01/23/2021 12:19:43 ****** Running HMMER to confirm orthology of predicted proteins: [hmmsearch] 146 of 146 task(s) completed at 01/23/2021 12:19:44 Results: C:85.8%[S:85.8%,D:0.0%],F:2.0%,M:12.2%,n:148 127 Complete BUSCOs (C) 127 Complete and single-copy BUSCOs (S) 0 Complete and duplicated BUSCOs (D) 3 Fragmented BUSCOs (F) 18 Missing BUSCOs (M) 148 Total BUSCO groups searched ****** Phase 2 of 2, predictions using species specific training ****** ****** Step 1/3, current time: 01/23/2021 12:19:44 ****** Extracting missing and fragmented buscos from the ancestral_variants file... Running tblastn, writing output to /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/run_spades/blast_output/tblastn_spades_missing_and_frag_rerun.tsv... [tblastn] 1 of 1 task(s) completed at 01/23/2021 12:19:45 Maximum number of candidate contig per BUSCO limited to: 3 Getting coordinates for candidate regions... ****** Step 2/3, current time: 01/23/2021 12:19:45 ****** Training Augustus using Single-Copy Complete BUSCOs: Converting predicted genes to short genbank files at 01/23/2021 12:19:45... All files converted to short genbank files, now running the training scripts at 01/23/2021 12:19:46... Pre-Augustus scaffold extraction... Re-running Augustus with the new metaparameters, number of target BUSCOs: 21 [augustus] 2 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 4 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 6 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 8 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 10 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 12 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 14 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 16 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 18 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 19 of 19 task(s) completed at 01/23/2021 12:19:47 Extracting predicted proteins... ****** Step 3/3, current time: 01/23/2021 12:19:48 ****** Running HMMER to confirm orthology of predicted proteins: [hmmsearch] 4 of 19 task(s) completed at 01/23/2021 12:19:48 [hmmsearch] 14 of 19 task(s) completed at 01/23/2021 12:19:48 [hmmsearch] 16 of 19 task(s) completed at 01/23/2021 12:19:48 [hmmsearch] 18 of 19 task(s) completed at 01/23/2021 12:19:48 [hmmsearch] 19 of 19 task(s) completed at 01/23/2021 12:19:48 Results: C:93.2%[S:93.2%,D:0.0%],F:0.7%,M:6.1%,n:148 138 Complete BUSCOs (C) 138 Complete and single-copy BUSCOs (S) 0 Complete and duplicated BUSCOs (D) 1 Fragmented BUSCOs (F) 9 Missing BUSCOs (M) 148 Total BUSCO groups searched BUSCO analysis done. Total running time: 34.92380428314209 seconds Results written in /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/run_spades/
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Created: 12th Nov 2021 at 23:24
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Version 1 (earliest) Created 12th Nov 2021 at 23:24 by Marko Petek
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https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
This project’s main objective was to identify novel Colorado potato beetle gene targets for the development of specific RNAi insecticides and further validate prospective targets using transcriptomics. The work included gene selection, establishment of double-stranded RNA (dsRNA) production methodology and the evaluation of dsRNAs’ insecticidal potential in CPB feeding laboratory and field trials.
Programme: NIBSys
Public web page: http://projects.nib.si/rnainval/
Start date: 1st Nov 2014
End date: 31st Oct 2017
Short Name: 03_Omics Title: Omics analysis of RNAi response in CPB Description: Transcriptomics and metagenome changes upon feeding CPB larvae with dsRNA Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_01_ns-dsRNA_trans, _S_02_metagenome_resp
Assays: _A_01-DNAisol, _A_01_RNA-Seq_dsEGFP-NGS, _A_02-DNASeq, _A_02_CLC-RNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _I_03_Omics-files, _S_01_ns-dsRNA_trans-files, _S_02_metagenome_resp-files
Short Name: 02_metagenome_resp Title: CPB gut microbiome response to dsRNA feeding Description: Response of CPB gut microbiome to dsRNA feeding on the level of microbe abundance Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_03_Omics
Assays: _A_01-DNAisol, _A_02-DNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _S_02_metagenome_resp-files
Short Name: 06_extr_bact-assembly Assay Class: DRY Assay Type: assembly Title: De novo genome assembly of bacteria Description: De novo genome assembly of bacteria from rcf-extracted shotgun metagenomics reads pISA Assay creation date: 2021-01-16 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_03_Omics
Study: _S_02_metagenome_resp
