/output/PW363_transrate_usingReference.log Version 1
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_04_TransRate
SEEK ID: https://testing.sysmo-db.org/data_files/1009?version=1
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output/PW363_transrate_usingReference.log
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[ INFO] 2019-10-08 13:22:43 : Loading assembly: /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_03.2_components/output/fasta_2_all-per-cv/stCuSTr-P_cds_all.fasta [ INFO] 2019-10-08 13:22:50 : Analysing assembly: /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_03.2_components/output/fasta_2_all-per-cv/stCuSTr-P_cds_all.fasta [ INFO] 2019-10-08 13:22:50 : Results will be saved in /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_04_transrate/output/PW363_transrate_usingReference/stCuSTr-P_cds_all [ INFO] 2019-10-08 13:22:50 : Calculating contig metrics... [ INFO] 2019-10-08 13:23:05 : Contig metrics: [ INFO] 2019-10-08 13:23:05 : ----------------------------------- [ INFO] 2019-10-08 13:23:05 : n seqs 159278 [ INFO] 2019-10-08 13:23:05 : smallest 93 [ INFO] 2019-10-08 13:23:05 : largest 10956 [ INFO] 2019-10-08 13:23:05 : n bases 125766519 [ INFO] 2019-10-08 13:23:05 : mean len 774.5 [ INFO] 2019-10-08 13:23:05 : n under 200 17370 [ INFO] 2019-10-08 13:23:05 : n over 1k 42571 [ INFO] 2019-10-08 13:23:05 : n over 10k 3 [ INFO] 2019-10-08 13:23:05 : n with orf 100222 [ INFO] 2019-10-08 13:23:05 : mean orf percent 99.79 [ INFO] 2019-10-08 13:23:05 : n90 429 [ INFO] 2019-10-08 13:23:05 : n70 771 [ INFO] 2019-10-08 13:23:05 : n50 1131 [ INFO] 2019-10-08 13:23:05 : n30 1596 [ INFO] 2019-10-08 13:23:05 : n10 2751 [ INFO] 2019-10-08 13:23:05 : gc 0.42 [ INFO] 2019-10-08 13:23:05 : gc skew 0.09 [ INFO] 2019-10-08 13:23:05 : at skew 0.02 [ INFO] 2019-10-08 13:23:05 : cpg ratio 1.48 [ INFO] 2019-10-08 13:23:05 : bases n 57119 [ INFO] 2019-10-08 13:23:05 : proportion n 0.0 [ INFO] 2019-10-08 13:23:05 : linguistic complexity 0.15 [ INFO] 2019-10-08 13:23:05 : Contig metrics done in 15 seconds [ INFO] 2019-10-08 13:23:05 : No reads provided, skipping read diagnostics [ INFO] 2019-10-08 13:23:05 : Calculating comparative metrics... [ INFO] 2019-10-08 13:24:07 : Comparative metrics: [ INFO] 2019-10-08 13:24:07 : ----------------------------------- [ INFO] 2019-10-08 13:24:07 : CRBB hits 116834 [ INFO] 2019-10-08 13:24:07 : n contigs with CRBB 116834 [ INFO] 2019-10-08 13:24:07 : p contigs with CRBB 0.73 [ INFO] 2019-10-08 13:24:07 : rbh per reference 2.37 [ INFO] 2019-10-08 13:24:07 : n refs with CRBB 23839 [ INFO] 2019-10-08 13:24:07 : p refs with CRBB 0.48 [ INFO] 2019-10-08 13:24:07 : cov25 22317 [ INFO] 2019-10-08 13:24:07 : p cov25 0.45 [ INFO] 2019-10-08 13:24:07 : cov50 20620 [ INFO] 2019-10-08 13:24:07 : p cov50 0.42 [ INFO] 2019-10-08 13:24:07 : cov75 18188 [ INFO] 2019-10-08 13:24:07 : p cov75 0.37 [ INFO] 2019-10-08 13:24:07 : cov85 16840 [ INFO] 2019-10-08 13:24:07 : p cov85 0.34 [ INFO] 2019-10-08 13:24:07 : cov95 14727 [ INFO] 2019-10-08 13:24:07 : p cov95 0.3 [ INFO] 2019-10-08 13:24:07 : reference coverage 0.54 [ INFO] 2019-10-08 13:24:07 : Comparative metrics done in 62 seconds [ INFO] 2019-10-08 13:24:07 : ----------------------------------- [ INFO] 2019-10-08 13:24:07 : Writing contig metrics for each contig to /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_04_transrate/output/PW363_transrate_usingReference/stCuSTr-P_cds_all/contigs.csv [ INFO] 2019-10-08 13:24:22 : Writing analysis results to assemblies.csv
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Created: 10th Nov 2019 at 23:15
Last updated: 10th Nov 2019 at 23:16
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Version 1 (earliest) Created 10th Nov 2019 at 23:15 by Andrej Blejec
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Institutions: National Institute of Biology, NIB, <script>alert('xss-institution-title')</script> & Test Institution
https://orcid.org/0000-0001-7484-6031
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Web page: Not specified
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 post filtering and reassignment TransRate post filtering and reassignment
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT-1
Study: _S_03_stCuSTr
