RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.8Is50H/RM_533111.MonSep81149252025
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: 1757357365
Database = /dev/shm/rModeler.8Is50H/GCA_000697605.1_RhiOryHUMC02-1.0 
  - Sequences = 2313
  - Bases = 40287170
  - N50 = 111252
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  504461-540479 |                                                   [ 1 ]
  468444-504461 |                                                   [  ]
  432427-468444 |                                                   [ 2 ]
  396409-432426 |                                                   [ 1 ]
  360392-396409 |                                                   [ 1 ]
  324375-360392 |                                                   [ 1 ]
  288358-324375 |                                                   [ 4 ]
  252340-288357 |                                                   [ 8 ]
  216323-252340 |                                                   [ 14 ]
  180306-216323 |                                                   [ 10 ]
  144289-180306 |                                                   [ 26 ]
  108271-144288 |*                                                  [ 42 ]
  72254-108271  |*                                                  [ 60 ]
  36237-72254   |***                                                [ 124 ]
  220-36237     |************************************************** [ 2019 ]

Storage Throughput = excellent ( 1081.47 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40287108 bp ( 39010819 non ambiguous )
   - Num Contigs Represented = 2313
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 395 raw families identified
   - RepeatScout: Running filtering stage.. 386 families remaining
   - RepeatScout: 00:04:56 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 372 families... 00:00:56 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 83 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time
Round Time: 00:06:06 (hh:mm:ss) Elapsed Time : 289 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 00:00:20 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4349 repeats masked totaling 1181169 bp(s).
   - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10365954 bp
       Num Contigs Represented = 708
       Non ambiguous bp:
             Initial: 10036003 bp
             After Masking: 8836523 bp
             Masked: 11.95 % 
 -- Input Database Coverage: 10365954 bp out of 40287170 bp ( 25.73 % )
Sampling Time: 00:00:46 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 304590
Comparison Time: 00:13:45 (hh:mm:ss) Elapsed Time, 6848 HSPs Collected
Number of families returned by RECON: 1614
Round Time: 00:14:47 (hh:mm:ss) Elapsed Time : 8 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       14022 repeats masked totaling 4008233 bp(s).
   - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29921121 bp
       Num Contigs Represented = 1769
       Non ambiguous bp:
             Initial: 28974783 bp
             After Masking: 24898124 bp
             Masked: 14.07 % 
 -- Input Database Coverage: 40287075 bp out of 40287170 bp ( 100.00 % )
Sampling Time: 00:02:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2412306
Comparison Time: 01:19:00 (hh:mm:ss) Elapsed Time, 38312 HSPs Collected
Number of families returned by RECON: 6502
Round Time: 01:22:43 (hh:mm:ss) Elapsed Time : 66 families discovered.

RepeatScout/RECON discovery complete: 363 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.8Is50H/RM_533111.MonSep81149252025
# 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: 00:01:46 (hh:mm:ss) Elapsed Time


Program Time: 01:45:22 (hh:mm:ss) Elapsed Time