RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.0ZGxY7/RM_1788850.ThuFeb120640392026
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: 1770907239
Database = /dev/shm/rModeler.0ZGxY7/GCA_027924085.1_AbraCBS73388_1.0 
  - Sequences = 1141
  - Bases = 35410303
  - N50 = 229910
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  821810-880475 |                                                   [ 1 ]
  763145-821810 |                                                   [  ]
  704480-763145 |                                                   [  ]
  645815-704480 |                                                   [  ]
  587150-645815 |                                                   [ 3 ]
  528485-587150 |                                                   [ 1 ]
  469820-528485 |                                                   [ 4 ]
  411155-469820 |                                                   [ 5 ]
  352490-411155 |                                                   [ 5 ]
  293825-352490 |                                                   [ 10 ]
  235160-293825 |                                                   [ 15 ]
  176495-235160 |*                                                  [ 22 ]
  117830-176495 |*                                                  [ 28 ]
  59165-117830  |***                                                [ 64 ]
  500-59165     |************************************************** [ 983 ]

Storage Throughput = excellent ( 1655.53 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 35410216 bp ( 35327491 non ambiguous )
   - Num Contigs Represented = 1141
   - 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.. : 16 raw families identified
   - RepeatScout: Running filtering stage.. 15 families remaining
   - RepeatScout: 00:00:36 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 14 families... 00:00:03 (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: 00:00:44 (hh:mm:ss) Elapsed Time : 14 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...
       137 repeats masked totaling 21458 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10030335 bp
       Num Contigs Represented = 418
       Non ambiguous bp:
             Initial: 10005203 bp
             After Masking: 9959810 bp
             Masked: 0.45 % 
 -- Input Database Coverage: 10030335 bp out of 35410303 bp ( 28.33 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 150426
Comparison Time: 00:04:11 (hh:mm:ss) Elapsed Time, 1754 HSPs Collected
Number of families returned by RECON: 723
Round Time: 00:04:27 (hh:mm:ss) Elapsed Time : 2 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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       499 repeats masked totaling 79277 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 25379801 bp
       Num Contigs Represented = 847
       Non ambiguous bp:
             Initial: 25322208 bp
             After Masking: 25193831 bp
             Masked: 0.51 % 
 -- Input Database Coverage: 35410136 bp out of 35410303 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 856086
Comparison Time: 00:13:05 (hh:mm:ss) Elapsed Time, 10603 HSPs Collected
Number of families returned by RECON: 2946
Round Time: 00:13:44 (hh:mm:ss) Elapsed Time : 9 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.0ZGxY7/RM_1788850.ThuFeb120640392026
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:19:01 (hh:mm:ss) Elapsed Time