output/quast/Enterobacter/busco_stats/run_spades.log Version 1
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
SEEK ID: https://fairdomhub.org/documents/2586?version=1
Filename:
output/quast/Enterobacter/busco_stats/run_spades.log
Format: Plain text document
Size: 5.27 KB
[hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H01Q4.faa.2 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H01NJ.faa.1 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H0041.faa.2 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H00J8.faa.3 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H02LW.faa.2 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H0220.faa.2 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H02FP.faa.1 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H00NK.faa.1 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H01SD.faa.2 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H00IF.faa.1 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H02KX.faa.1 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H00ZY.faa.2 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H01FV.faa.2 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H02FP.faa.3 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H01JZ.faa.2 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H0444.faa.2 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H02DK.faa.2 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H00NK.faa.3 for reading [hmmsearch] Error: Failed to open sequence file /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/augustus_output/extracted_proteins/POG091H01RS.faa.2 for reading missing and fragmented buscos from the ancestral_variants file... Running tblastn, writing output to /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/blast_output/tblastn_spades_missing_and_frag_rerun.tsv... [tblastn] 1 of 1 task(s) completed at 01/24/2021 16:14:55 Maximum number of candidate contig per BUSCO limited to: 3 Getting coordinates for candidate regions... ****** Step 2/3, current time: 01/24/2021 16:14:55 ****** Training Augustus using Single-Copy Complete BUSCOs: Converting predicted genes to short genbank files at 01/24/2021 16:14:55... All files converted to short genbank files, now running the training scripts at 01/24/2021 16:14:56... Pre-Augustus scaffold extraction... Re-running Augustus with the new metaparameters, number of target BUSCOs: 70 [augustus] 70 of 138 task(s) completed at 01/24/2021 16:14:57 [augustus] 83 of 138 task(s) completed at 01/24/2021 16:14:57 [augustus] 111 of 138 task(s) completed at 01/24/2021 16:14:57 [augustus] 125 of 138 task(s) completed at 01/24/2021 16:14:57 [augustus] 138 of 138 task(s) completed at 01/24/2021 16:14:57 Extracting predicted proteins... ****** Step 3/3, current time: 01/24/2021 16:15:00 ****** Running HMMER to confirm orthology of predicted proteins: [hmmsearch] 59 of 84 task(s) completed at 01/24/2021 16:15:01 [hmmsearch] 76 of 84 task(s) completed at 01/24/2021 16:15:01 [hmmsearch] 84 of 84 task(s) completed at 01/24/2021 16:15:01 Results: C:54.8%[S:50.7%,D:4.1%],F:16.2%,M:29.0%,n:148 81 Complete BUSCOs (C) 75 Complete and single-copy BUSCOs (S) 6 Complete and duplicated BUSCOs (D) 24 Fragmented BUSCOs (F) 43 Missing BUSCOs (M) 148 Total BUSCO groups searched BUSCO analysis done. Total running time: 38.35190987586975 seconds Results written in /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterobacter/busco_stats/run_spades/
Export PNG
Creators and Submitter
Views: 839 Downloads: 39
Created: 12th Nov 2021 at 23:21
Last updated: 12th Nov 2021 at 23:21
AttributionsNone
Version History
Version 1 (earliest) Created 12th Nov 2021 at 23:21 by Marko Petek
No revision comments
Related items
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
