RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.3BlCNN/RM_158662.ThuFeb120648262026
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: 1770907705
Database = /dev/shm/rModeler.3BlCNN/GCA_027924065.1_AbraIFM66951_1.0 
  - Sequences = 1206
  - Bases = 36136287
  - N50 = 184316
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  829698-888927 |                                                   [ 1 ]
  770470-829698 |                                                   [  ]
  711241-770469 |                                                   [ 1 ]
  652013-711241 |                                                   [  ]
  592784-652012 |                                                   [ 1 ]
  533556-592784 |                                                   [ 3 ]
  474327-533555 |                                                   [ 2 ]
  415099-474327 |                                                   [ 4 ]
  355870-415098 |                                                   [ 6 ]
  296642-355870 |                                                   [ 5 ]
  237413-296641 |                                                   [ 12 ]
  178185-237413 |*                                                  [ 21 ]
  118956-178184 |*                                                  [ 40 ]
  59728-118956  |***                                                [ 74 ]
  500-59728     |************************************************** [ 1036 ]

Storage Throughput = excellent ( 1667.63 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36136192 bp ( 36039634 non ambiguous )
   - Num Contigs Represented = 1206
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 24 raw families identified
   - RepeatScout: Running filtering stage.. 21 families remaining
   - RepeatScout: 00:00:38 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:45 (hh:mm:ss) Elapsed Time : 16 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       227 repeats masked totaling 36820 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10035875 bp
       Num Contigs Represented = 412
       Non ambiguous bp:
             Initial: 10009658 bp
             After Masking: 9952699 bp
             Masked: 0.57 % 
 -- Input Database Coverage: 10035875 bp out of 36136287 bp ( 27.77 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 139656
Comparison Time: 00:04:05 (hh:mm:ss) Elapsed Time, 2139 HSPs Collected
Number of families returned by RECON: 775
Round Time: 00:04:17 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       554 repeats masked totaling 92127 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26100245 bp
       Num Contigs Represented = 926
       Non ambiguous bp:
             Initial: 26029904 bp
             After Masking: 25883565 bp
             Masked: 0.56 % 
 -- Input Database Coverage: 36136120 bp out of 36136287 bp ( 100.00 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 969528
Comparison Time: 00:13:57 (hh:mm:ss) Elapsed Time, 11734 HSPs Collected
Number of families returned by RECON: 3181
Round Time: 00:14:42 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.3BlCNN/RM_158662.ThuFeb120648262026
# 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: 00:00:07 (hh:mm:ss) Elapsed Time


Program Time: 00:19:51 (hh:mm:ss) Elapsed Time