RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.SXYrO8/RM_1764296.FriSep120906302025
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: 1757693190
Database = /dev/shm/rModeler.SXYrO8/GCA_040256725.1_ASM4025672v1 
  - Sequences = 12
  - Bases = 36611222
Storage Throughput = excellent ( 1689.77 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36611158 bp ( 36607158 non ambiguous )
   - Num Contigs Represented = 12
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 229 raw families identified
   - RepeatScout: Running filtering stage.. 218 families remaining
   - RepeatScout: 00:01:38 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 209 families... 00:15:14 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 satellite(s), 62 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:16:59 (hh:mm:ss) Elapsed Time : 147 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 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4052 repeats masked totaling 2043482 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10029075 bp
       Num Contigs Represented = 12
       Non ambiguous bp:
             Initial: 10028075 bp
             After Masking: 7955448 bp
             Masked: 20.67 % 
 -- Input Database Coverage: 10029075 bp out of 36611222 bp ( 27.39 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31626
Comparison Time: 00:03:27 (hh:mm:ss) Elapsed Time, 6795 HSPs Collected
Number of families returned by RECON: 1158
Round Time: 00:03:52 (hh:mm:ss) Elapsed Time : 9 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       11478 repeats masked totaling 5660428 bp(s).
   - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26582060 bp
       Num Contigs Represented = 12
       Non ambiguous bp:
             Initial: 26579060 bp
             After Masking: 20838726 bp
             Masked: 21.60 % 
 -- Input Database Coverage: 36611135 bp out of 36611222 bp ( 100.00 % )
Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 224785
Comparison Time: 00:12:36 (hh:mm:ss) Elapsed Time, 18419 HSPs Collected
Number of families returned by RECON: 4593
Round Time: 00:13:45 (hh:mm:ss) Elapsed Time : 14 families discovered.

RepeatScout/RECON discovery complete: 170 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.SXYrO8/RM_1764296.FriSep120906302025
# 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: 00:00:34 (hh:mm:ss) Elapsed Time


Program Time: 00:35:10 (hh:mm:ss) Elapsed Time