RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.ADlquT/RM_2354062.ThuSep110736422025
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: 1757601401
Database = /dev/shm/rModeler.ADlquT/GCA_023629915.1_ASM2362991v1 
  - Sequences = 398
  - Bases = 30301216
  - N50 = 292160
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1188628-1273495 |                                                   [ 1 ]
  1103762-1188628 |                                                   [  ]
  1018896-1103762 |                                                   [  ]
  934030-1018896  |                                                   [ 1 ]
  849164-934030   |                                                   [ 1 ]
  764298-849164   |                                                   [ 1 ]
  679432-764298   |                                                   [  ]
  594565-679431   |                                                   [ 2 ]
  509699-594565   |                                                   [ 3 ]
  424833-509699   |                                                   [ 4 ]
  339967-424833   |*                                                  [ 10 ]
  255101-339967   |*                                                  [ 11 ]
  170235-255101   |***                                                [ 20 ]
  85369-170235    |*******                                            [ 46 ]
  503-85369       |************************************************** [ 298 ]

Storage Throughput = excellent ( 1752.11 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 30301151 bp ( 30299164 non ambiguous )
   - Num Contigs Represented = 398
   - 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.. : 150 raw families identified
   - RepeatScout: Running filtering stage.. 149 families remaining
   - RepeatScout: 00:00:52 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 141 families... 00:00:18 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 48 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:14 (hh:mm:ss) Elapsed Time : 93 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1563 repeats masked totaling 408579 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10037926 bp
       Num Contigs Represented = 203
       Non ambiguous bp:
             Initial: 10037328 bp
             After Masking: 9608964 bp
             Masked: 4.27 % 
 -- Input Database Coverage: 10037926 bp out of 30301216 bp ( 33.13 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 60726
Comparison Time: 00:04:38 (hh:mm:ss) Elapsed Time, 13853 HSPs Collected
Number of families returned by RECON: 1739
Round Time: 00:05:00 (hh:mm:ss) Elapsed Time : 3 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3754 repeats masked totaling 1086991 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 20263199 bp
       Num Contigs Represented = 304
       Non ambiguous bp:
             Initial: 20261810 bp
             After Masking: 19128786 bp
             Masked: 5.59 % 
 -- Input Database Coverage: 30301125 bp out of 30301216 bp ( 100.00 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 233586
Comparison Time: 00:11:12 (hh:mm:ss) Elapsed Time, 22308 HSPs Collected
Number of families returned by RECON: 4382
Round Time: 00:11:58 (hh:mm:ss) Elapsed Time : 12 families discovered.

RepeatScout/RECON discovery complete: 108 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.ADlquT/RM_2354062.ThuSep110736422025
# 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: 00:00:15 (hh:mm:ss) Elapsed Time


Program Time: 00:18:27 (hh:mm:ss) Elapsed Time