RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.USYs61/RM_3343601.WedFeb111108302026
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: 1770836909
Database = /data/tmp/rModeler.USYs61/GCA_023845535.1_PKCLINC048 
  - Sequences = 47
  - Bases = 24811993
Storage Throughput = good ( 871.54 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 24811890 bp ( 24532214 non ambiguous )
   - Num Contigs Represented = 47
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 173 raw families identified
   - RepeatScout: Running filtering stage.. 70 families remaining
   - RepeatScout: 00:04:15 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 69 families... 00:00:39 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 19 contained, found in 00:00:05 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:05 (hh:mm:ss) Elapsed Time
Round Time: 00:05:07 (hh:mm:ss) Elapsed Time : 49 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:02:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3376 repeats masked totaling 517534 bp(s).
   - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10154847 bp
       Num Contigs Represented = 25
       Non ambiguous bp:
             Initial: 10032768 bp
             After Masking: 8603005 bp
             Masked: 14.25 % 
 -- Input Database Coverage: 10154847 bp out of 24811993 bp ( 40.93 % )
Sampling Time: 00:02:23 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 34453
Comparison Time: 00:24:44 (hh:mm:ss) Elapsed Time, 24975 HSPs Collected
Number of families returned by RECON: 1338
Round Time: 00:31:12 (hh:mm:ss) Elapsed Time : 23 families discovered.
   - Increasing sample size to include end piece now = 44811993


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 44811993 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:03:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6542 repeats masked totaling 1119809 bp(s).
   - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 14656977 bp
       Num Contigs Represented = 38
       Non ambiguous bp:
             Initial: 14499380 bp
             After Masking: 12107409 bp
             Masked: 16.50 % 
 -- Input Database Coverage: 24811824 bp out of 24811993 bp ( 100.00 % )
Sampling Time: 00:03:43 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 75466
Comparison Time: 00:38:09 (hh:mm:ss) Elapsed Time, 5896 HSPs Collected
Number of families returned by RECON: 1591
Round Time: 00:43:20 (hh:mm:ss) Elapsed Time : 6 families discovered.

RepeatScout/RECON discovery complete: 78 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.USYs61/RM_3343601.WedFeb111108302026
# 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: 00:00:39 (hh:mm:ss) Elapsed Time


Program Time: 01:20:18 (hh:mm:ss) Elapsed Time