/output/PGSC_DM_v3.4_transcript-update_representative_transrate_usingReference.log Version 1
_p_stRT/_I_STRT/_S_04_stPanTr/_A_06_tr_rep-transrate
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output/PGSC_DM_v3.4_transcript-update_representative_transrate_usingReference.log
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[ INFO] 2020-02-05 10:57:39 : Loading assembly: /DATA/majaz/_stRT_revision/_A_transrate_rep/input/PGSC_DM_v3.4_transcript-update_representative.fasta [ INFO] 2020-02-05 10:57:42 : Analysing assembly: /DATA/majaz/_stRT_revision/_A_transrate_rep/input/PGSC_DM_v3.4_transcript-update_representative.fasta [ INFO] 2020-02-05 10:57:42 : Results will be saved in /DATA/majaz/_stRT_revision/_A_transrate_rep/output/PGSC_DM_v3.4_transcript-update_representative_transrate_usingReference/PGSC_DM_v3.4_transcript-update_representative [ INFO] 2020-02-05 10:57:42 : Calculating contig metrics... [ INFO] 2020-02-05 10:57:46 : Contig metrics: [ INFO] 2020-02-05 10:57:46 : ----------------------------------- [ INFO] 2020-02-05 10:57:46 : n seqs 39031 [ INFO] 2020-02-05 10:57:46 : smallest 51 [ INFO] 2020-02-05 10:57:46 : largest 8888 [ INFO] 2020-02-05 10:57:46 : n bases 50078136 [ INFO] 2020-02-05 10:57:46 : mean len 1282.67 [ INFO] 2020-02-05 10:57:46 : n under 200 87 [ INFO] 2020-02-05 10:57:46 : n over 1k 20226 [ INFO] 2020-02-05 10:57:46 : n over 10k 0 [ INFO] 2020-02-05 10:57:46 : n with orf 28325 [ INFO] 2020-02-05 10:57:46 : mean orf percent 73.1 [ INFO] 2020-02-05 10:57:46 : n90 645 [ INFO] 2020-02-05 10:57:46 : n70 1217 [ INFO] 2020-02-05 10:57:46 : n50 1726 [ INFO] 2020-02-05 10:57:46 : n30 2353 [ INFO] 2020-02-05 10:57:46 : n10 3535 [ INFO] 2020-02-05 10:57:46 : gc 0.4 [ INFO] 2020-02-05 10:57:46 : gc skew 0.08 [ INFO] 2020-02-05 10:57:46 : at skew 0.01 [ INFO] 2020-02-05 10:57:46 : cpg ratio 1.47 [ INFO] 2020-02-05 10:57:46 : bases n 41291 [ INFO] 2020-02-05 10:57:46 : proportion n 0.0 [ INFO] 2020-02-05 10:57:46 : linguistic complexity 0.22 [ INFO] 2020-02-05 10:57:46 : Contig metrics done in 5 seconds [ INFO] 2020-02-05 10:57:46 : No reads provided, skipping read diagnostics [ INFO] 2020-02-05 10:57:46 : Calculating comparative metrics... [ INFO] 2020-02-05 10:58:23 : Comparative metrics: [ INFO] 2020-02-05 10:58:23 : ----------------------------------- [ INFO] 2020-02-05 10:58:23 : CRBB hits 38600 [ INFO] 2020-02-05 10:58:23 : n contigs with CRBB 38600 [ INFO] 2020-02-05 10:58:23 : p contigs with CRBB 0.99 [ INFO] 2020-02-05 10:58:23 : rbh per reference 0.78 [ INFO] 2020-02-05 10:58:23 : n refs with CRBB 37534 [ INFO] 2020-02-05 10:58:23 : p refs with CRBB 0.76 [ INFO] 2020-02-05 10:58:23 : cov25 37387 [ INFO] 2020-02-05 10:58:23 : p cov25 0.76 [ INFO] 2020-02-05 10:58:23 : cov50 36379 [ INFO] 2020-02-05 10:58:23 : p cov50 0.74 [ INFO] 2020-02-05 10:58:23 : cov75 33634 [ INFO] 2020-02-05 10:58:23 : p cov75 0.68 [ INFO] 2020-02-05 10:58:23 : cov85 32200 [ INFO] 2020-02-05 10:58:23 : p cov85 0.65 [ INFO] 2020-02-05 10:58:23 : cov95 30187 [ INFO] 2020-02-05 10:58:23 : p cov95 0.61 [ INFO] 2020-02-05 10:58:23 : reference coverage 0.75 [ INFO] 2020-02-05 10:58:23 : Comparative metrics done in 36 seconds [ INFO] 2020-02-05 10:58:23 : ----------------------------------- [ INFO] 2020-02-05 10:58:23 : Writing contig metrics for each contig to /DATA/majaz/_stRT_revision/_A_transrate_rep/output/PGSC_DM_v3.4_transcript-update_representative_transrate_usingReference/PGSC_DM_v3.4_transcript-update_representative/contigs.csv [ INFO] 2020-02-05 10:58:26 : Writing analysis results to assemblies.csv
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Created: 19th Mar 2020 at 11:00
Last updated: 19th Mar 2020 at 11:00
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Version 1 (earliest) Created 19th Mar 2020 at 11:00 by Andrej Blejec
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Related items
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, INDIE - Biotechnological production of sustainable indole, _p_stRT, Public project, Playground, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture
Institutions: National Institute of Biology, NewHorizon
https://orcid.org/0000-0001-7484-6031
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
project: _p_stRT Short Name: stRT Title: Solanum tuberosum Reference Transcriptomes Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato pISA projects path: ../pISA-Projects Local pISA-tree organisation: National Institute of Biology pISA project creation date: 2019-10-22 pISA project creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Project funding code: This project was supported by the Slovenian Research Agency (grants P4-0165, J4-4165, J4-7636, ...
Programme: NIBSys
Public web page: http://www.nib.si/eng/index.php/systems-biology
Start date: 1st Dec 2017
End date: 1st Jan 2020
Investigation: _I_STRT Short Name: STRT Title: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Phenodata: ./phenodata_20191022.txt pISA Investigation creation date: 2019-10-22 pISA Investigation creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes
RELATED ...
Submitter: Maja Zagorscak
Studies: SupplementaryInformation, _S_01_sequences, _S_02_denovo, _S_03_stCuSTr, _S_04_stPanTr
Assays: Supplementary Information, _A_01_GC_content-count, _A_01_evigene, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _A_02.3_InterProScan, _A_02.4_STAR, _A_02.5_STARlong_matchAnnot, _A_02.6_TransRate, _A_02.7_VecScreen, _A_02.8_DIAMOND, _A_02_cdhit_3cvs-GFFmerged, _A_03.1_filtering, _A_03.2_components, _A_03_components_3cvs-GFFmerged, _A_04_BUSCO_3cvs-GFFmerged, _A_04_TransRate, _A_05_BUSCO, _A_05_MSA_3cvs-GFFmerged, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged
Short Name: 04_stPanTr Title: Solanum tuberosum Pan-Transcriptome Description: Solanum tuberosum Pan-Transcriptome Raw Data: pISA Study creation date: 2019-10-22 pISA Study creator: Maja Zagorscak Principal investigator: Kristina Gruden License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Investigation: _I_STRT
Assays: _A_01_GC_content-count, _A_02_cdhit_3cvs-GFFmerged, _A_03_components_3cvs-GFFmerged, _A_04_BUSCO_3cvs-GFFmerged, _A_05_MSA_3cvs-GFFmerged, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged
Short Name: 06_tr_rep-transrate Assay Class: DRY Assay Type: transrate Title: Cultivar representative transcriptome transrate Description: Transrate on cultivar specific representatives, GFF merged as a reference for CRRB pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_04_stPanTr
