/output/stCuSTr-P_tr_representatives_transrate_usingReference.log

Version 1

[ INFO] 2020-02-05 11:02:28 : Loading assembly: /DATA/majaz/_stRT_revision/_A_transrate_rep/input/stCuSTr-P_tr_representatives.fasta
[ INFO] 2020-02-05 11:02:30 : Analysing assembly: /DATA/majaz/_stRT_revision/_A_transrate_rep/input/stCuSTr-P_tr_representatives.fasta
[ INFO] 2020-02-05 11:02:30 : Results will be saved in /DATA/majaz/_stRT_revision/_A_transrate_rep/output/stCuSTr-P_tr_representatives_transrate_usingReference/stCuSTr-P_tr_representatives
[ INFO] 2020-02-05 11:02:30 : Calculating contig metrics...
[ INFO] 2020-02-05 11:02:35 : Contig metrics:
[ INFO] 2020-02-05 11:02:35 : -----------------------------------
[ INFO] 2020-02-05 11:02:35 : n seqs                        43883
[ INFO] 2020-02-05 11:02:35 : smallest                        103
[ INFO] 2020-02-05 11:02:35 : largest                       14444
[ INFO] 2020-02-05 11:02:35 : n bases                    40880451
[ INFO] 2020-02-05 11:02:35 : mean len                     926.21
[ INFO] 2020-02-05 11:02:35 : n under 200                    1377
[ INFO] 2020-02-05 11:02:35 : n over 1k                     14545
[ INFO] 2020-02-05 11:02:35 : n over 10k                        6
[ INFO] 2020-02-05 11:02:35 : n with orf                    20125
[ INFO] 2020-02-05 11:02:35 : mean orf percent              75.34
[ INFO] 2020-02-05 11:02:35 : n90                             387
[ INFO] 2020-02-05 11:02:35 : n70                             964
[ INFO] 2020-02-05 11:02:35 : n50                            1535
[ INFO] 2020-02-05 11:02:35 : n30                            2170
[ INFO] 2020-02-05 11:02:35 : n10                            3530
[ INFO] 2020-02-05 11:02:35 : gc                             0.41
[ INFO] 2020-02-05 11:02:35 : gc skew                        0.01
[ INFO] 2020-02-05 11:02:35 : at skew                        -0.0
[ INFO] 2020-02-05 11:02:35 : cpg ratio                      1.47
[ INFO] 2020-02-05 11:02:35 : bases n                       35200
[ INFO] 2020-02-05 11:02:35 : proportion n                    0.0
[ INFO] 2020-02-05 11:02:35 : linguistic complexity          0.17
[ INFO] 2020-02-05 11:02:35 : Contig metrics done in 5 seconds
[ INFO] 2020-02-05 11:02:35 : No reads provided, skipping read diagnostics
[ INFO] 2020-02-05 11:02:35 : Calculating comparative metrics...
[ INFO] 2020-02-05 11:02:56 : Comparative metrics:
[ INFO] 2020-02-05 11:02:56 : -----------------------------------
[ INFO] 2020-02-05 11:02:56 : CRBB hits                     30826
[ INFO] 2020-02-05 11:02:56 : n contigs with CRBB           30826
[ INFO] 2020-02-05 11:02:56 : p contigs with CRBB             0.7
[ INFO] 2020-02-05 11:02:56 : rbh per reference              0.62
[ INFO] 2020-02-05 11:02:56 : n refs with CRBB              21751
[ INFO] 2020-02-05 11:02:56 : p refs with CRBB               0.44
[ INFO] 2020-02-05 11:02:56 : cov25                         12295
[ INFO] 2020-02-05 11:02:56 : p cov25                        0.25
[ INFO] 2020-02-05 11:02:56 : cov50                         10693
[ INFO] 2020-02-05 11:02:56 : p cov50                        0.22
[ INFO] 2020-02-05 11:02:56 : cov75                          8850
[ INFO] 2020-02-05 11:02:56 : p cov75                        0.18
[ INFO] 2020-02-05 11:02:56 : cov85                          7848
[ INFO] 2020-02-05 11:02:56 : p cov85                        0.16
[ INFO] 2020-02-05 11:02:56 : cov95                          6430
[ INFO] 2020-02-05 11:02:56 : p cov95                        0.13
[ INFO] 2020-02-05 11:02:56 : reference coverage             0.28
[ INFO] 2020-02-05 11:02:56 : Comparative metrics done in 21 seconds
[ INFO] 2020-02-05 11:02:56 : -----------------------------------
[ INFO] 2020-02-05 11:02:56 : Writing contig metrics for each contig to /DATA/majaz/_stRT_revision/_A_transrate_rep/output/stCuSTr-P_tr_representatives_transrate_usingReference/stCuSTr-P_tr_representatives/contigs.csv
[ INFO] 2020-02-05 11:02:59 : Writing analysis results to assemblies.csv