/output/Rywal_transrate_usingReference.log Version 1
_p_stRT/_I_STRT/_S_03_stCuSTr/_A_04_TransRate
SEEK ID: https://testing.sysmo-db.org/data_files/1011?version=1
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output/Rywal_transrate_usingReference.log
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[ INFO] 2019-10-08 13:24:26 : Loading assembly: /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_03.2_components/output/fasta_2_all-per-cv/stCuSTr-R_cds_all.fasta [ INFO] 2019-10-08 13:24:29 : Analysing assembly: /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_03.2_components/output/fasta_2_all-per-cv/stCuSTr-R_cds_all.fasta [ INFO] 2019-10-08 13:24:29 : Results will be saved in /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_04_transrate/output/Rywal_transrate_usingReference/stCuSTr-R_cds_all [ INFO] 2019-10-08 13:24:29 : Calculating contig metrics... [ INFO] 2019-10-08 13:24:36 : Contig metrics: [ INFO] 2019-10-08 13:24:36 : ----------------------------------- [ INFO] 2019-10-08 13:24:36 : n seqs 79095 [ INFO] 2019-10-08 13:24:36 : smallest 93 [ INFO] 2019-10-08 13:24:36 : largest 10551 [ INFO] 2019-10-08 13:24:36 : n bases 57757872 [ INFO] 2019-10-08 13:24:36 : mean len 707.4 [ INFO] 2019-10-08 13:24:36 : n under 200 13198 [ INFO] 2019-10-08 13:24:36 : n over 1k 18748 [ INFO] 2019-10-08 13:24:36 : n over 10k 1 [ INFO] 2019-10-08 13:24:36 : n with orf 41523 [ INFO] 2019-10-08 13:24:36 : mean orf percent 99.78 [ INFO] 2019-10-08 13:24:36 : n90 390 [ INFO] 2019-10-08 13:24:36 : n70 750 [ INFO] 2019-10-08 13:24:36 : n50 1218 [ INFO] 2019-10-08 13:24:36 : n30 1797 [ INFO] 2019-10-08 13:24:36 : n10 3111 [ INFO] 2019-10-08 13:24:36 : gc 0.42 [ INFO] 2019-10-08 13:24:36 : gc skew 0.09 [ INFO] 2019-10-08 13:24:36 : at skew 0.02 [ INFO] 2019-10-08 13:24:36 : cpg ratio 1.49 [ INFO] 2019-10-08 13:24:36 : bases n 27963 [ INFO] 2019-10-08 13:24:36 : proportion n 0.0 [ INFO] 2019-10-08 13:24:36 : linguistic complexity 0.14 [ INFO] 2019-10-08 13:24:36 : Contig metrics done in 7 seconds [ INFO] 2019-10-08 13:24:36 : No reads provided, skipping read diagnostics [ INFO] 2019-10-08 13:24:36 : Calculating comparative metrics... [ INFO] 2019-10-08 13:25:10 : Comparative metrics: [ INFO] 2019-10-08 13:25:10 : ----------------------------------- [ INFO] 2019-10-08 13:25:10 : CRBB hits 55239 [ INFO] 2019-10-08 13:25:10 : n contigs with CRBB 55239 [ INFO] 2019-10-08 13:25:10 : p contigs with CRBB 0.7 [ INFO] 2019-10-08 13:25:10 : rbh per reference 1.12 [ INFO] 2019-10-08 13:25:10 : n refs with CRBB 22163 [ INFO] 2019-10-08 13:25:10 : p refs with CRBB 0.45 [ INFO] 2019-10-08 13:25:10 : cov25 20978 [ INFO] 2019-10-08 13:25:10 : p cov25 0.43 [ INFO] 2019-10-08 13:25:10 : cov50 19538 [ INFO] 2019-10-08 13:25:10 : p cov50 0.4 [ INFO] 2019-10-08 13:25:10 : cov75 17370 [ INFO] 2019-10-08 13:25:10 : p cov75 0.35 [ INFO] 2019-10-08 13:25:10 : cov85 16288 [ INFO] 2019-10-08 13:25:10 : p cov85 0.33 [ INFO] 2019-10-08 13:25:10 : cov95 14470 [ INFO] 2019-10-08 13:25:10 : p cov95 0.29 [ INFO] 2019-10-08 13:25:10 : reference coverage 0.52 [ INFO] 2019-10-08 13:25:10 : Comparative metrics done in 33 seconds [ INFO] 2019-10-08 13:25:10 : ----------------------------------- [ INFO] 2019-10-08 13:25:10 : Writing contig metrics for each contig to /DATA/majaz/_I_STRT/_S_03_stCuSTr/_A_04_transrate/output/Rywal_transrate_usingReference/stCuSTr-R_cds_all/contigs.csv [ INFO] 2019-10-08 13:25:16 : Writing analysis results to assemblies.csv
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Created: 10th Nov 2019 at 23:16
Last updated: 10th Nov 2019 at 23:16
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Version 1 (earliest) Created 10th Nov 2019 at 23:16 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 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
