RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.stCJoH/RM_1261477.MonSep81307352025
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: 1757362055
Database = /data/tmp/rModeler.stCJoH/GCA_000974265.2_CS3270v5.4 
  - Sequences = 26
  - Bases = 37070975
Storage Throughput = good ( 914.57 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37070837 bp ( 37064537 non ambiguous )
   - Num Contigs Represented = 26
   - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 39 raw families identified
   - RepeatScout: Running filtering stage.. 22 families remaining
   - RepeatScout: 00:01:15 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 20 families... 00:00:08 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:01:41 (hh:mm:ss) Elapsed Time : 18 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       288 repeats masked totaling 39984 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10033112 bp
       Num Contigs Represented = 6
       Non ambiguous bp:
             Initial: 10031512 bp
             After Masking: 9971376 bp
             Masked: 0.60 % 
 -- Input Database Coverage: 10033112 bp out of 37070975 bp ( 27.06 % )
Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31626
Comparison Time: 00:13:38 (hh:mm:ss) Elapsed Time, 35085 HSPs Collected
Number of families returned by RECON: 836
Round Time: 01:21:28 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       958 repeats masked totaling 374973 bp(s).
   - TE Masking time 00:02:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27037645 bp
       Num Contigs Represented = 24
       Non ambiguous bp:
             Initial: 27032945 bp
             After Masking: 26618289 bp
             Masked: 1.53 % 
 -- Input Database Coverage: 37070757 bp out of 37070975 bp ( 100.00 % )
Sampling Time: 00:03:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 238395
Comparison Time: 00:37:32 (hh:mm:ss) Elapsed Time, 201460 HSPs Collected
Number of families returned by RECON: 3290
Round Time: 02:54:37 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 30 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.stCJoH/RM_1261477.MonSep81307352025
# 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: 00:00:37 (hh:mm:ss) Elapsed Time


Program Time: 04:18:23 (hh:mm:ss) Elapsed Time