RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.gnAfGx/RM_1201038.ThuSep112121422025
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: 1757650901
Database = /dev/shm/rModeler.gnAfGx/GCA_027604005.1_ASM2760400v1 
  - Sequences = 3354
  - Bases = 31510542
  - N50 = 39537
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  255926-274170 |                                                   [ 1 ]
  237682-255925 |                                                   [  ]
  219438-237681 |                                                   [  ]
  201194-219437 |                                                   [ 1 ]
  182950-201193 |                                                   [ 1 ]
  164706-182949 |                                                   [ 3 ]
  146462-164705 |                                                   [ 3 ]
  128219-146462 |                                                   [ 7 ]
  109975-128218 |                                                   [ 9 ]
  91731-109974  |                                                   [ 20 ]
  73487-91730   |                                                   [ 35 ]
  55243-73486   |                                                   [ 48 ]
  36999-55242   |*                                                  [ 108 ]
  18755-36998   |**                                                 [ 172 ]
  512-18755     |************************************************** [ 2946 ]

Storage Throughput = excellent ( 1661.75 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 31510474 bp ( 31464834 non ambiguous )
   - Num Contigs Represented = 3354
   - 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.. : 77 raw families identified
   - RepeatScout: Running filtering stage.. 74 families remaining
   - RepeatScout: 00:00:51 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 71 families... 00:00:09 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 19 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:04 (hh:mm:ss) Elapsed Time : 52 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       712 repeats masked totaling 153790 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10047247 bp
       Num Contigs Represented = 1187
       Non ambiguous bp:
             Initial: 10033034 bp
             After Masking: 9801460 bp
             Masked: 2.31 % 
 -- Input Database Coverage: 10047247 bp out of 31510542 bp ( 31.89 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 755835
Comparison Time: 00:07:28 (hh:mm:ss) Elapsed Time, 3879 HSPs Collected
Number of families returned by RECON: 1170
Round Time: 00:08:17 (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 00:00:23 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2004 repeats masked totaling 533920 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 21463193 bp
       Num Contigs Represented = 2283
       Non ambiguous bp:
             Initial: 21431766 bp
             After Masking: 20739742 bp
             Masked: 3.23 % 
 -- Input Database Coverage: 31510440 bp out of 31510542 bp ( 100.00 % )
Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2948806
Comparison Time: 00:18:21 (hh:mm:ss) Elapsed Time, 16223 HSPs Collected
Number of families returned by RECON: 3279
Round Time: 00:19:20 (hh:mm:ss) Elapsed Time : 25 families discovered.

RepeatScout/RECON discovery complete: 79 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.gnAfGx/RM_1201038.ThuSep112121422025
# 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: 00:00:11 (hh:mm:ss) Elapsed Time


Program Time: 00:28:52 (hh:mm:ss) Elapsed Time