/output/stCuSTr-R_tr_representatives_transrate_usingReference.log

Version 1

[ INFO] 2020-02-05 11:01:55 : Loading assembly: /DATA/majaz/_stRT_revision/_A_transrate_rep/input/stCuSTr-R_tr_representatives.fasta
[ INFO] 2020-02-05 11:01:56 : Analysing assembly: /DATA/majaz/_stRT_revision/_A_transrate_rep/input/stCuSTr-R_tr_representatives.fasta
[ INFO] 2020-02-05 11:01:56 : Results will be saved in /DATA/majaz/_stRT_revision/_A_transrate_rep/output/stCuSTr-R_tr_representatives_transrate_usingReference/stCuSTr-R_tr_representatives
[ INFO] 2020-02-05 11:01:56 : Calculating contig metrics...
[ INFO] 2020-02-05 11:02:00 : Contig metrics:
[ INFO] 2020-02-05 11:02:00 : -----------------------------------
[ INFO] 2020-02-05 11:02:00 : n seqs                        36336
[ INFO] 2020-02-05 11:02:00 : smallest                        100
[ INFO] 2020-02-05 11:02:00 : largest                       13016
[ INFO] 2020-02-05 11:02:00 : n bases                    37552131
[ INFO] 2020-02-05 11:02:00 : mean len                     1027.5
[ INFO] 2020-02-05 11:02:00 : n under 200                    1310
[ INFO] 2020-02-05 11:02:00 : n over 1k                     14307
[ INFO] 2020-02-05 11:02:00 : n over 10k                        2
[ INFO] 2020-02-05 11:02:00 : n with orf                    19034
[ INFO] 2020-02-05 11:02:00 : mean orf percent              76.16
[ INFO] 2020-02-05 11:02:00 : n90                             440
[ INFO] 2020-02-05 11:02:00 : n70                            1139
[ INFO] 2020-02-05 11:02:00 : n50                            1673
[ INFO] 2020-02-05 11:02:00 : n30                            2286
[ INFO] 2020-02-05 11:02:00 : n10                            3502
[ INFO] 2020-02-05 11:02:00 : gc                             0.41
[ INFO] 2020-02-05 11:02:00 : gc skew                       -0.01
[ INFO] 2020-02-05 11:02:00 : at skew                        -0.0
[ INFO] 2020-02-05 11:02:00 : cpg ratio                      1.48
[ INFO] 2020-02-05 11:02:00 : bases n                       28835
[ INFO] 2020-02-05 11:02:00 : proportion n                    0.0
[ INFO] 2020-02-05 11:02:00 : linguistic complexity          0.18
[ INFO] 2020-02-05 11:02:00 : Contig metrics done in 4 seconds
[ INFO] 2020-02-05 11:02:00 : No reads provided, skipping read diagnostics
[ INFO] 2020-02-05 11:02:00 : Calculating comparative metrics...
[ INFO] 2020-02-05 11:02:20 : Comparative metrics:
[ INFO] 2020-02-05 11:02:20 : -----------------------------------
[ INFO] 2020-02-05 11:02:20 : CRBB hits                     28389
[ INFO] 2020-02-05 11:02:20 : n contigs with CRBB           28389
[ INFO] 2020-02-05 11:02:20 : p contigs with CRBB            0.78
[ INFO] 2020-02-05 11:02:20 : rbh per reference              0.58
[ INFO] 2020-02-05 11:02:20 : n refs with CRBB              21299
[ INFO] 2020-02-05 11:02:20 : p refs with CRBB               0.43
[ INFO] 2020-02-05 11:02:20 : cov25                          9140
[ INFO] 2020-02-05 11:02:20 : p cov25                        0.19
[ INFO] 2020-02-05 11:02:20 : cov50                          7909
[ INFO] 2020-02-05 11:02:20 : p cov50                        0.16
[ INFO] 2020-02-05 11:02:20 : cov75                          6585
[ INFO] 2020-02-05 11:02:20 : p cov75                        0.13
[ INFO] 2020-02-05 11:02:20 : cov85                          5951
[ INFO] 2020-02-05 11:02:20 : p cov85                        0.12
[ INFO] 2020-02-05 11:02:20 : cov95                          5053
[ INFO] 2020-02-05 11:02:20 : p cov95                         0.1
[ INFO] 2020-02-05 11:02:20 : reference coverage              0.2
[ INFO] 2020-02-05 11:02:20 : Comparative metrics done in 20 seconds
[ INFO] 2020-02-05 11:02:20 : -----------------------------------
[ INFO] 2020-02-05 11:02:20 : Writing contig metrics for each contig to /DATA/majaz/_stRT_revision/_A_transrate_rep/output/stCuSTr-R_tr_representatives_transrate_usingReference/stCuSTr-R_tr_representatives/contigs.csv
[ INFO] 2020-02-05 11:02:24 : Writing analysis results to assemblies.csv