RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.YQrrU7/RM_1928053.ThuSep110401562025
Search Engine = rmblast 2.14.1+
Threads = 32
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1757588516
Database = /data/tmp/rModeler.YQrrU7/GCA_023212765.1_ASM2321276v1 
  - Sequences = 158
  - Bases = 19488417
  - N50 = 305106
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  924774-990756 |*                                                  [ 2 ]
  858792-924773 |                                                   [  ]
  792811-858792 |                                                   [  ]
  726829-792810 |                                                   [ 1 ]
  660848-726829 |                                                   [ 1 ]
  594866-660847 |                                                   [  ]
  528885-594866 |*                                                  [ 3 ]
  462903-528884 |                                                   [ 1 ]
  396922-462903 |***                                                [ 5 ]
  330940-396921 |*                                                  [ 3 ]
  264959-330940 |****                                               [ 8 ]
  198977-264958 |****                                               [ 8 ]
  132996-198977 |*********                                          [ 15 ]
  67014-132995  |******************                                 [ 30 ]
  1033-67014    |************************************************** [ 81 ]

Storage Throughput = excellent ( 1551.85 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19488264 bp ( 19486583 non ambiguous )
   - Num Contigs Represented = 158
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 13 raw families identified
   - RepeatScout: Running filtering stage.. 13 families remaining
   - RepeatScout: 00:00:38 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 13 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:47 (hh:mm:ss) Elapsed Time : 13 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       307 repeats masked totaling 47312 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10020049 bp
       Num Contigs Represented = 115
       Non ambiguous bp:
             Initial: 10019223 bp
             After Masking: 9908514 bp
             Masked: 1.10 % 
 -- Input Database Coverage: 10020049 bp out of 19488417 bp ( 51.42 % )
Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 45150
Comparison Time: 00:05:21 (hh:mm:ss) Elapsed Time, 17790 HSPs Collected
Number of families returned by RECON: 1501
Round Time: 00:05:53 (hh:mm:ss) Elapsed Time : 5 families discovered.
   - Increasing sample size to include end piece now = 39488417


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39488417 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2311 repeats masked totaling 248411 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9468143 bp
       Num Contigs Represented = 111
       Non ambiguous bp:
             Initial: 9467288 bp
             After Masking: 9161217 bp
             Masked: 3.23 % 
 -- Input Database Coverage: 19488192 bp out of 19488417 bp ( 100.00 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 41041
Comparison Time: 00:05:20 (hh:mm:ss) Elapsed Time, 2613 HSPs Collected
Number of families returned by RECON: 716
Round Time: 00:05:44 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 19 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.YQrrU7/RM_1928053.ThuSep110401562025
# Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib
#   - 18011 proteins
# Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib
#   - 26292 consensus sequences
  - Looking for simple/tandem and low complexity sequences..
  - Looking for similarity to known repeat proteins..
  - Looking for similarity to known repeat consensi..

Classification Time: 00:00:09 (hh:mm:ss) Elapsed Time


Program Time: 00:12:33 (hh:mm:ss) Elapsed Time