/output/stCuSTr-D_tr_representatives_transrate_usingReference.log

Version 1

[ INFO] 2020-02-05 11:03:07 : Loading assembly: /DATA/majaz/_stRT_revision/_A_transrate_rep/input/stCuSTr-D_tr_representatives.fasta
[ INFO] 2020-02-05 11:03:09 : Analysing assembly: /DATA/majaz/_stRT_revision/_A_transrate_rep/input/stCuSTr-D_tr_representatives.fasta
[ INFO] 2020-02-05 11:03:09 : Results will be saved in /DATA/majaz/_stRT_revision/_A_transrate_rep/output/stCuSTr-D_tr_representatives_transrate_usingReference/stCuSTr-D_tr_representatives
[ INFO] 2020-02-05 11:03:09 : Calculating contig metrics...
[ INFO] 2020-02-05 11:03:15 : Contig metrics:
[ INFO] 2020-02-05 11:03:15 : -----------------------------------
[ INFO] 2020-02-05 11:03:15 : n seqs                        57943
[ INFO] 2020-02-05 11:03:15 : smallest                        100
[ INFO] 2020-02-05 11:03:15 : largest                       15690
[ INFO] 2020-02-05 11:03:15 : n bases                    53549281
[ INFO] 2020-02-05 11:03:15 : mean len                     921.65
[ INFO] 2020-02-05 11:03:15 : n under 200                     875
[ INFO] 2020-02-05 11:03:15 : n over 1k                     18500
[ INFO] 2020-02-05 11:03:15 : n over 10k                       13
[ INFO] 2020-02-05 11:03:15 : n with orf                    24260
[ INFO] 2020-02-05 11:03:15 : mean orf percent               72.6
[ INFO] 2020-02-05 11:03:15 : n90                             369
[ INFO] 2020-02-05 11:03:15 : n70                             943
[ INFO] 2020-02-05 11:03:15 : n50                            1566
[ INFO] 2020-02-05 11:03:15 : n30                            2221
[ INFO] 2020-02-05 11:03:15 : n10                            3620
[ INFO] 2020-02-05 11:03:15 : gc                              0.4
[ INFO] 2020-02-05 11:03:15 : gc skew                        0.01
[ INFO] 2020-02-05 11:03:15 : at skew                        -0.0
[ INFO] 2020-02-05 11:03:15 : cpg ratio                      1.46
[ INFO] 2020-02-05 11:03:15 : bases n                       39277
[ INFO] 2020-02-05 11:03:15 : proportion n                    0.0
[ INFO] 2020-02-05 11:03:15 : linguistic complexity          0.17
[ INFO] 2020-02-05 11:03:15 : Contig metrics done in 6 seconds
[ INFO] 2020-02-05 11:03:15 : No reads provided, skipping read diagnostics
[ INFO] 2020-02-05 11:03:15 : Calculating comparative metrics...
[ INFO] 2020-02-05 11:03:43 : Comparative metrics:
[ INFO] 2020-02-05 11:03:43 : -----------------------------------
[ INFO] 2020-02-05 11:03:43 : CRBB hits                     38034
[ INFO] 2020-02-05 11:03:43 : n contigs with CRBB           38034
[ INFO] 2020-02-05 11:03:43 : p contigs with CRBB            0.66
[ INFO] 2020-02-05 11:03:43 : rbh per reference              0.77
[ INFO] 2020-02-05 11:03:43 : n refs with CRBB              25094
[ INFO] 2020-02-05 11:03:43 : p refs with CRBB               0.51
[ INFO] 2020-02-05 11:03:43 : cov25                         14354
[ INFO] 2020-02-05 11:03:43 : p cov25                        0.29
[ INFO] 2020-02-05 11:03:43 : cov50                         12799
[ INFO] 2020-02-05 11:03:43 : p cov50                        0.26
[ INFO] 2020-02-05 11:03:43 : cov75                         10767
[ INFO] 2020-02-05 11:03:43 : p cov75                        0.22
[ INFO] 2020-02-05 11:03:43 : cov85                          9682
[ INFO] 2020-02-05 11:03:43 : p cov85                         0.2
[ INFO] 2020-02-05 11:03:43 : cov95                          8053
[ INFO] 2020-02-05 11:03:43 : p cov95                        0.16
[ INFO] 2020-02-05 11:03:43 : reference coverage             0.33
[ INFO] 2020-02-05 11:03:43 : Comparative metrics done in 28 seconds
[ INFO] 2020-02-05 11:03:43 : -----------------------------------
[ INFO] 2020-02-05 11:03:43 : Writing contig metrics for each contig to /DATA/majaz/_stRT_revision/_A_transrate_rep/output/stCuSTr-D_tr_representatives_transrate_usingReference/stCuSTr-D_tr_representatives/contigs.csv
[ INFO] 2020-02-05 11:03:48 : Writing analysis results to assemblies.csv