RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.bXrNT7/RM_1734393.ThuSep110151312025
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: 1757580691
Database = /dev/shm/rModeler.bXrNT7/GCA_022385745.1_Leisp1 
  - Sequences = 549
  - Bases = 34515440
  - N50 = 195173
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  717299-768463 |                                                   [ 3 ]
  666135-717298 |                                                   [  ]
  614971-666134 |                                                   [ 3 ]
  563807-614970 |                                                   [ 1 ]
  512643-563806 |                                                   [ 1 ]
  461479-512642 |                                                   [ 3 ]
  410315-461478 |                                                   [ 1 ]
  359151-410314 |                                                   [ 5 ]
  307987-359150 |                                                   [ 6 ]
  256823-307986 |                                                   [ 5 ]
  205659-256822 |*                                                  [ 14 ]
  154495-205658 |***                                                [ 28 ]
  103331-154494 |****                                               [ 38 ]
  52167-103330  |******                                             [ 51 ]
  1004-52167    |************************************************** [ 390 ]

Storage Throughput = excellent ( 1636.11 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 34515316 bp ( 34478197 non ambiguous )
   - Num Contigs Represented = 549
   - 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.. : 73 raw families identified
   - RepeatScout: Running filtering stage.. 72 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 67 families... 00:00:09 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 8 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:51 (hh:mm:ss) Elapsed Time : 59 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       485 repeats masked totaling 166672 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10052238 bp
       Num Contigs Represented = 249
       Non ambiguous bp:
             Initial: 10038130 bp
             After Masking: 9864003 bp
             Masked: 1.73 % 
 -- Input Database Coverage: 10052238 bp out of 34515440 bp ( 29.12 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 67528
Comparison Time: 00:04:35 (hh:mm:ss) Elapsed Time, 2446 HSPs Collected
Number of families returned by RECON: 818
Round Time: 00:04:57 (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 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1234 repeats masked totaling 398934 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 24463032 bp
       Num Contigs Represented = 422
       Non ambiguous bp:
             Initial: 24440021 bp
             After Masking: 24018266 bp
             Masked: 1.73 % 
 -- Input Database Coverage: 34515270 bp out of 34515440 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 372816
Comparison Time: 00:13:52 (hh:mm:ss) Elapsed Time, 12719 HSPs Collected
Number of families returned by RECON: 2724
Round Time: 00:14:26 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 72 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.bXrNT7/RM_1734393.ThuSep110151312025
# 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: 00:20:23 (hh:mm:ss) Elapsed Time