RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.nRmMAc/RM_408659.FriSep121619152025
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: 1757719154
Database = /dev/shm/rModeler.nRmMAc/GCA_047301375.1_ASM4730137v1 
  - Sequences = 25
  - Bases = 25244836
Storage Throughput = excellent ( 1096.75 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 25244750 bp ( 25244750 non ambiguous )
   - Num Contigs Represented = 25
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 19 raw families identified
   - RepeatScout: Running filtering stage.. 18 families remaining
   - RepeatScout: 00:01:54 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 17 families... 00:34:55 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 2 satellite(s), 1 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:36:59 (hh:mm:ss) Elapsed Time : 14 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       520 repeats masked totaling 734644 bp(s).
   - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10016910 bp
       Num Contigs Represented = 16
       Non ambiguous bp:
             Initial: 10016910 bp
             After Masking: 9231320 bp
             Masked: 7.84 % 
 -- Input Database Coverage: 10016910 bp out of 25244836 bp ( 39.68 % )
Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32385
Comparison Time: 00:06:45 (hh:mm:ss) Elapsed Time, 6272 HSPs Collected
Number of families returned by RECON: 535
Round Time: 00:12:05 (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 : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       742 repeats masked totaling 1051790 bp(s).
   - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 15227760 bp
       Num Contigs Represented = 16
       Non ambiguous bp:
             Initial: 15227760 bp
             After Masking: 14102865 bp
             Masked: 7.39 % 
 -- Input Database Coverage: 25244670 bp out of 25244836 bp ( 100.00 % )
Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 75078
Comparison Time: 00:12:19 (hh:mm:ss) Elapsed Time, 6283 HSPs Collected
Number of families returned by RECON: 1015
Round Time: 00:13:21 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 18 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.nRmMAc/RM_408659.FriSep121619152025
# 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: 00:00:33 (hh:mm:ss) Elapsed Time


Program Time: 01:02:58 (hh:mm:ss) Elapsed Time