RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.K4mYtQ/RM_1667519.ThuSep110145552025
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: 1757580355
Database = /dev/shm/rModeler.K4mYtQ/GCA_022288595.1_ASM2228859v1 
  - Sequences = 1630
  - Bases = 29917063
  - N50 = 36968
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  263739-282506 |                                                   [ 1 ]
  244972-263738 |                                                   [  ]
  226205-244971 |                                                   [ 1 ]
  207438-226204 |                                                   [  ]
  188672-207438 |                                                   [  ]
  169905-188671 |                                                   [ 1 ]
  151138-169904 |                                                   [  ]
  132371-151137 |                                                   [ 2 ]
  113604-132370 |                                                   [ 11 ]
  94838-113604  |                                                   [ 10 ]
  76071-94837   |                                                   [ 16 ]
  57304-76070   |**                                                 [ 52 ]
  38537-57303   |*****                                              [ 130 ]
  19770-38536   |************                                       [ 281 ]
  1004-19770    |************************************************** [ 1125 ]

Storage Throughput = excellent ( 1685.12 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 29916950 bp ( 29907592 non ambiguous )
   - Num Contigs Represented = 1630
   - 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.. : 116 raw families identified
   - RepeatScout: Running filtering stage.. 114 families remaining
   - RepeatScout: 00:00:46 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 108 families... 00:00:15 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 21 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:05 (hh:mm:ss) Elapsed Time : 87 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1722 repeats masked totaling 498495 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10008218 bp
       Num Contigs Represented = 618
       Non ambiguous bp:
             Initial: 10005136 bp
             After Masking: 9473015 bp
             Masked: 5.32 % 
 -- Input Database Coverage: 10008218 bp out of 29917063 bp ( 33.45 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 214185
Comparison Time: 00:05:22 (hh:mm:ss) Elapsed Time, 16275 HSPs Collected
Number of families returned by RECON: 1731
Round Time: 00:05:48 (hh:mm:ss) Elapsed Time : 30 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6017 repeats masked totaling 1126510 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 19908679 bp
       Num Contigs Represented = 1107
       Non ambiguous bp:
             Initial: 19902403 bp
             After Masking: 18705394 bp
             Masked: 6.01 % 
 -- Input Database Coverage: 29916897 bp out of 29917063 bp ( 100.00 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 766941
Comparison Time: 00:11:44 (hh:mm:ss) Elapsed Time, 24459 HSPs Collected
Number of families returned by RECON: 3173
Round Time: 00:12:29 (hh:mm:ss) Elapsed Time : 55 families discovered.

RepeatScout/RECON discovery complete: 172 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.K4mYtQ/RM_1667519.ThuSep110145552025
# 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: 00:19:37 (hh:mm:ss) Elapsed Time