RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.Kqofqv/RM_13814.TueAug130022452024
Search Engine = rmblast 2.13.0+
Threads = 32
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1723533764
Database = /dev/shm/rModeler.Kqofqv/GCA_003014415.1_Cand_auris_B11243   - Sequences = 238
  - Bases = 12354602
  - N50 = 86899
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  307354-329236 |*                                                  [ 2 ]
  285472-307353 |                                                   [  ]
  263591-285472 |*                                                  [ 2 ]
  241709-263590 |                                                   [ 1 ]
  219827-241708 |*                                                  [ 2 ]
  197946-219827 |*                                                  [ 3 ]
  176064-197945 |**                                                 [ 5 ]
  154182-176063 |*                                                  [ 2 ]
  132301-154182 |**                                                 [ 4 ]
  110419-132300 |***                                                [ 6 ]
  88537-110418  |*****                                              [ 9 ]
  66656-88537   |***************                                    [ 27 ]
  44774-66655   |************                                       [ 23 ]
  22892-44773   |**********************************                 [ 62 ]
  1011-22892    |************************************************** [ 90 ]

Storage Throughput = excellent ( 1013.39 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 12354527 bp ( 12350766 non ambiguous )
   - Num Contigs Represented = 238
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:06:34 (hh:mm:ss) Elapsed Time
Round Time: 00:06:54 (hh:mm:ss) Elapsed Time : 7 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       201 repeats masked totaling 34770 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10037281 bp
       Num Contigs Represented = 209
       Non ambiguous bp:
             Initial: 10034166 bp
             After Masking: 9974985 bp
             Masked: 0.59 % 
 -- Input Database Coverage: 10037281 bp out of 12354602 bp ( 81.24 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 63903
Comparison Time: 00:07:51 (hh:mm:ss) Elapsed Time, 3258 HSPs Collected
Number of families returned by RECON: 860
Round Time: 00:08:21 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 32354602


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 32354602 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       46 repeats masked totaling 6937 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2317239 bp
       Num Contigs Represented = 76
       Non ambiguous bp:
             Initial: 2316593 bp
             After Masking: 2303016 bp
             Masked: 0.59 % 
 -- Input Database Coverage: 12354520 bp out of 12354602 bp ( 100.00 % )
Sampling Time: 00:00:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 3828
Comparison Time: 00:01:08 (hh:mm:ss) Elapsed Time, 150 HSPs Collected
Number of families returned by RECON: 73
Round Time: 00:01:13 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 10 families found


Classification Time: 00:00:23 (hh:mm:ss) Elapsed Time


Program Time: 00:16:51 (hh:mm:ss) Elapsed Time