/output/Desiree_initial_transrate_usingReference.log Version 1
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_02.6_TransRate
SEEK ID: https://testing.sysmo-db.org/data_files/1189?version=1
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output/Desiree_initial_transrate_usingReference.log
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[ INFO] 2019-10-08 20:00:24 : Loading assembly: /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_02.6_transrate/input/Desiree.cds [ INFO] 2019-10-08 20:00:44 : Analysing assembly: /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_02.6_transrate/input/Desiree.cds [ INFO] 2019-10-08 20:00:44 : Results will be saved in /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_02.6_transrate/output/Desiree_initial_transrate_usingReference/Desiree [ INFO] 2019-10-08 20:00:44 : Calculating contig metrics... [ INFO] 2019-10-08 20:01:14 : Contig metrics: [ INFO] 2019-10-08 20:01:14 : ----------------------------------- [ INFO] 2019-10-08 20:01:14 : n seqs 350271 [ INFO] 2019-10-08 20:01:14 : smallest 93 [ INFO] 2019-10-08 20:01:14 : largest 15315 [ INFO] 2019-10-08 20:01:14 : n bases 193804749 [ INFO] 2019-10-08 20:01:14 : mean len 504.5 [ INFO] 2019-10-08 20:01:14 : n under 200 125465 [ INFO] 2019-10-08 20:01:14 : n over 1k 57679 [ INFO] 2019-10-08 20:01:14 : n over 10k 23 [ INFO] 2019-10-08 20:01:14 : n with orf 132959 [ INFO] 2019-10-08 20:01:14 : mean orf percent 99.75 [ INFO] 2019-10-08 20:01:14 : n90 369 [ INFO] 2019-10-08 20:01:14 : n70 753 [ INFO] 2019-10-08 20:01:14 : n50 1194 [ INFO] 2019-10-08 20:01:14 : n30 1797 [ INFO] 2019-10-08 20:01:14 : n10 5100 [ INFO] 2019-10-08 20:01:14 : gc 0.41 [ INFO] 2019-10-08 20:01:14 : gc skew 0.07 [ INFO] 2019-10-08 20:01:14 : at skew 0.02 [ INFO] 2019-10-08 20:01:14 : cpg ratio 1.47 [ INFO] 2019-10-08 20:01:14 : bases n 81812 [ INFO] 2019-10-08 20:01:14 : proportion n 0.0 [ INFO] 2019-10-08 20:01:14 : linguistic complexity 0.11 [ INFO] 2019-10-08 20:01:14 : Contig metrics done in 31 seconds [ INFO] 2019-10-08 20:01:14 : No reads provided, skipping read diagnostics [ INFO] 2019-10-08 20:01:14 : Calculating comparative metrics... [ INFO] 2019-10-08 20:03:36 : Comparative metrics: [ INFO] 2019-10-08 20:03:36 : ----------------------------------- [ INFO] 2019-10-08 20:03:36 : CRBB hits 160295 [ INFO] 2019-10-08 20:03:36 : n contigs with CRBB 160295 [ INFO] 2019-10-08 20:03:36 : p contigs with CRBB 0.46 [ INFO] 2019-10-08 20:03:36 : rbh per reference 3.25 [ INFO] 2019-10-08 20:03:36 : n refs with CRBB 29858 [ INFO] 2019-10-08 20:03:36 : p refs with CRBB 0.61 [ INFO] 2019-10-08 20:03:36 : cov25 27856 [ INFO] 2019-10-08 20:03:36 : p cov25 0.56 [ INFO] 2019-10-08 20:03:36 : cov50 25991 [ INFO] 2019-10-08 20:03:36 : p cov50 0.53 [ INFO] 2019-10-08 20:03:36 : cov75 23309 [ INFO] 2019-10-08 20:03:36 : p cov75 0.47 [ INFO] 2019-10-08 20:03:36 : cov85 21828 [ INFO] 2019-10-08 20:03:36 : p cov85 0.44 [ INFO] 2019-10-08 20:03:36 : cov95 19329 [ INFO] 2019-10-08 20:03:36 : p cov95 0.39 [ INFO] 2019-10-08 20:03:36 : reference coverage 0.65 [ INFO] 2019-10-08 20:03:36 : Comparative metrics done in 141 seconds [ INFO] 2019-10-08 20:03:36 : ----------------------------------- [ INFO] 2019-10-08 20:03:36 : Writing contig metrics for each contig to /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_02.6_transrate/output/Desiree_initial_transrate_usingReference/Desiree/contigs.csv [ INFO] 2019-10-08 20:04:01 : Writing analysis results to assemblies.csv
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Created: 13th Nov 2019 at 22:30
Last updated: 13th Nov 2019 at 22:30
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Version 1 (earliest) Created 13th Nov 2019 at 22:30 by Andrej Blejec
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Institutions: National Institute of Biology, NIB, <script>alert('xss-institution-title')</script> & Test Institution
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Investigation: _I_STRT\n Short Name: STRT\n 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 Principal investigator: Kristina Gruden License: GPL-3 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Studies: _S_01_sequences, _S_02_denovo, _S_03_stCuSTr, _S_04_stPanTr
Assays: _A_01_evigene, _A_01_evigene_1_3cvs-gffmerged, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _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_components_1_3cvs-gffmerged, _A_03.1_filtering, _A_03.2_components, _A_03_BUSCO_1_3cvs-gffmerged, _A_04-MSA, _A_04_TransRate, _A_05_BUSCO, _A_05_BUSCO-Stat, _A_05_BUSCO-Stat-old, _A__S_01_sequences-files, _A__S_02_denovo-files, _A__S_03_stCuSTr-files, _A__S_04_stPanTr-files
Submitter: Andrej Blejec
Investigation: _I_STRT-1
Assays: _A_01_evigene, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _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_03.1_filtering, _A_03.2_components, _A_04_TransRate, _A_05_BUSCO, _A__S_03_stCuSTr-files
TransRate stat on raw tr2aacds transcriptomes TransRate stat on raw tr2aacds transcriptomes, basic and reference-based
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT-1
Study: _S_03_stCuSTr
