/output/Rywal_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/892?version=1
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output/Rywal_initial_transrate_usingReference.log
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[ INFO] 2019-10-08 20:06:59 : Loading assembly: /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_02.6_transrate/input/Rywal.cds [ INFO] 2019-10-08 20:07:06 : Analysing assembly: /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_02.6_transrate/input/Rywal.cds [ INFO] 2019-10-08 20:07:06 : Results will be saved in /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_02.6_transrate/output/Rywal_initial_transrate_usingReference/Rywal [ INFO] 2019-10-08 20:07:06 : Calculating contig metrics... [ INFO] 2019-10-08 20:07:15 : Contig metrics: [ INFO] 2019-10-08 20:07:15 : ----------------------------------- [ INFO] 2019-10-08 20:07:15 : n seqs 134755 [ INFO] 2019-10-08 20:07:15 : smallest 93 [ INFO] 2019-10-08 20:07:15 : largest 10551 [ INFO] 2019-10-08 20:07:15 : n bases 68870376 [ INFO] 2019-10-08 20:07:15 : mean len 458.61 [ INFO] 2019-10-08 20:07:15 : n under 200 52653 [ INFO] 2019-10-08 20:07:15 : n over 1k 19175 [ INFO] 2019-10-08 20:07:15 : n over 10k 1 [ INFO] 2019-10-08 20:07:15 : n with orf 43870 [ INFO] 2019-10-08 20:07:15 : mean orf percent 99.74 [ INFO] 2019-10-08 20:07:15 : n90 351 [ INFO] 2019-10-08 20:07:15 : n70 693 [ INFO] 2019-10-08 20:07:15 : n50 1227 [ INFO] 2019-10-08 20:07:15 : n30 1944 [ INFO] 2019-10-08 20:07:15 : n10 10551 [ INFO] 2019-10-08 20:07:15 : gc 0.42 [ INFO] 2019-10-08 20:07:15 : gc skew 0.07 [ INFO] 2019-10-08 20:07:15 : at skew 0.01 [ INFO] 2019-10-08 20:07:15 : cpg ratio 1.48 [ INFO] 2019-10-08 20:07:15 : bases n 40673 [ INFO] 2019-10-08 20:07:15 : proportion n 0.0 [ INFO] 2019-10-08 20:07:15 : linguistic complexity 0.1 [ INFO] 2019-10-08 20:07:15 : Contig metrics done in 10 seconds [ INFO] 2019-10-08 20:07:15 : No reads provided, skipping read diagnostics [ INFO] 2019-10-08 20:07:15 : Calculating comparative metrics... [ INFO] 2019-10-08 20:08:10 : Comparative metrics: [ INFO] 2019-10-08 20:08:10 : ----------------------------------- [ INFO] 2019-10-08 20:08:10 : CRBB hits 66258 [ INFO] 2019-10-08 20:08:10 : n contigs with CRBB 66258 [ INFO] 2019-10-08 20:08:10 : p contigs with CRBB 0.49 [ INFO] 2019-10-08 20:08:10 : rbh per reference 1.34 [ INFO] 2019-10-08 20:08:10 : n refs with CRBB 23549 [ INFO] 2019-10-08 20:08:10 : p refs with CRBB 0.48 [ INFO] 2019-10-08 20:08:10 : cov25 21842 [ INFO] 2019-10-08 20:08:10 : p cov25 0.44 [ INFO] 2019-10-08 20:08:10 : cov50 20258 [ INFO] 2019-10-08 20:08:10 : p cov50 0.41 [ INFO] 2019-10-08 20:08:10 : cov75 18036 [ INFO] 2019-10-08 20:08:10 : p cov75 0.37 [ INFO] 2019-10-08 20:08:10 : cov85 16906 [ INFO] 2019-10-08 20:08:10 : p cov85 0.34 [ INFO] 2019-10-08 20:08:10 : cov95 14967 [ INFO] 2019-10-08 20:08:10 : p cov95 0.3 [ INFO] 2019-10-08 20:08:10 : reference coverage 0.53 [ INFO] 2019-10-08 20:08:10 : Comparative metrics done in 55 seconds [ INFO] 2019-10-08 20:08:10 : ----------------------------------- [ INFO] 2019-10-08 20:08:10 : Writing contig metrics for each contig to /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_02.6_transrate/output/Rywal_initial_transrate_usingReference/Rywal/contigs.csv [ INFO] 2019-10-08 20:08:19 : Writing analysis results to assemblies.csv
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Created: 10th Nov 2019 at 23:09
Last updated: 10th Nov 2019 at 23:09
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Version 1 (earliest) Created 10th Nov 2019 at 23:09 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
