/output/PW363_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/1191?version=1
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output/PW363_initial_transrate_usingReference.log
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[ INFO] 2019-10-08 20:04:04 : Loading assembly: /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_02.6_transrate/input/PW363.cds [ INFO] 2019-10-08 20:04:20 : Analysing assembly: /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_02.6_transrate/input/PW363.cds [ INFO] 2019-10-08 20:04:20 : Results will be saved in /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_02.6_transrate/output/PW363_initial_transrate_usingReference/PW363 [ INFO] 2019-10-08 20:04:20 : Calculating contig metrics... [ INFO] 2019-10-08 20:04:42 : Contig metrics: [ INFO] 2019-10-08 20:04:42 : ----------------------------------- [ INFO] 2019-10-08 20:04:42 : n seqs 273216 [ INFO] 2019-10-08 20:04:42 : smallest 93 [ INFO] 2019-10-08 20:04:42 : largest 10956 [ INFO] 2019-10-08 20:04:42 : n bases 152921568 [ INFO] 2019-10-08 20:04:42 : mean len 515.91 [ INFO] 2019-10-08 20:04:42 : n under 200 88230 [ INFO] 2019-10-08 20:04:42 : n over 1k 44508 [ INFO] 2019-10-08 20:04:42 : n over 10k 3 [ INFO] 2019-10-08 20:04:42 : n with orf 109649 [ INFO] 2019-10-08 20:04:42 : mean orf percent 99.74 [ INFO] 2019-10-08 20:04:42 : n90 366 [ INFO] 2019-10-08 20:04:42 : n70 702 [ INFO] 2019-10-08 20:04:42 : n50 1110 [ INFO] 2019-10-08 20:04:42 : n30 1659 [ INFO] 2019-10-08 20:04:42 : n10 4047 [ INFO] 2019-10-08 20:04:42 : gc 0.42 [ INFO] 2019-10-08 20:04:42 : gc skew 0.08 [ INFO] 2019-10-08 20:04:42 : at skew 0.02 [ INFO] 2019-10-08 20:04:42 : cpg ratio 1.47 [ INFO] 2019-10-08 20:04:42 : bases n 77040 [ INFO] 2019-10-08 20:04:42 : proportion n 0.0 [ INFO] 2019-10-08 20:04:42 : linguistic complexity 0.11 [ INFO] 2019-10-08 20:04:42 : Contig metrics done in 23 seconds [ INFO] 2019-10-08 20:04:42 : No reads provided, skipping read diagnostics [ INFO] 2019-10-08 20:04:42 : Calculating comparative metrics... [ INFO] 2019-10-08 20:06:36 : Comparative metrics: [ INFO] 2019-10-08 20:06:36 : ----------------------------------- [ INFO] 2019-10-08 20:06:36 : CRBB hits 138443 [ INFO] 2019-10-08 20:06:36 : n contigs with CRBB 138443 [ INFO] 2019-10-08 20:06:36 : p contigs with CRBB 0.51 [ INFO] 2019-10-08 20:06:36 : rbh per reference 2.81 [ INFO] 2019-10-08 20:06:36 : n refs with CRBB 25739 [ INFO] 2019-10-08 20:06:36 : p refs with CRBB 0.52 [ INFO] 2019-10-08 20:06:36 : cov25 23721 [ INFO] 2019-10-08 20:06:36 : p cov25 0.48 [ INFO] 2019-10-08 20:06:36 : cov50 21875 [ INFO] 2019-10-08 20:06:36 : p cov50 0.44 [ INFO] 2019-10-08 20:06:36 : cov75 19402 [ INFO] 2019-10-08 20:06:36 : p cov75 0.39 [ INFO] 2019-10-08 20:06:36 : cov85 17972 [ INFO] 2019-10-08 20:06:36 : p cov85 0.36 [ INFO] 2019-10-08 20:06:36 : cov95 15664 [ INFO] 2019-10-08 20:06:36 : p cov95 0.32 [ INFO] 2019-10-08 20:06:36 : reference coverage 0.56 [ INFO] 2019-10-08 20:06:36 : Comparative metrics done in 114 seconds [ INFO] 2019-10-08 20:06:36 : ----------------------------------- [ INFO] 2019-10-08 20:06:36 : Writing contig metrics for each contig to /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_02.6_transrate/output/PW363_initial_transrate_usingReference/PW363/contigs.csv [ INFO] 2019-10-08 20:06:54 : Writing analysis results to assemblies.csv
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Views: 1410 Downloads: 41
Created: 13th Nov 2019 at 22:30
Last updated: 13th Nov 2019 at 22:30
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Version History
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
