RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.W2gYJK/RM_2364683.WedFeb111110092026
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: 1770837008
Database = /dev/shm/rModeler.W2gYJK/GCA_023845545.1_PKCLINC047 
  - Sequences = 62
  - Bases = 24171523
Storage Throughput = excellent ( 1589.79 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 24171392 bp ( 23631396 non ambiguous )
   - Num Contigs Represented = 62
   - 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.. : 150 raw families identified
   - RepeatScout: Running filtering stage.. 69 families remaining
   - RepeatScout: 00:01:15 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 68 families... 00:00:15 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 satellite(s), 17 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:01:35 (hh:mm:ss) Elapsed Time : 50 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 00:00:44 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2976 repeats masked totaling 477534 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10178532 bp
       Num Contigs Represented = 36
       Non ambiguous bp:
             Initial: 10017662 bp
             After Masking: 8881056 bp
             Masked: 11.35 % 
 -- Input Database Coverage: 10178532 bp out of 24171523 bp ( 42.11 % )
Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 37128
Comparison Time: 00:13:45 (hh:mm:ss) Elapsed Time, 9911 HSPs Collected
Number of families returned by RECON: 1313
Round Time: 00:14:59 (hh:mm:ss) Elapsed Time : 12 families discovered.
   - Increasing sample size to include end piece now = 44171523


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 44171523 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:01 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5811 repeats masked totaling 964672 bp(s).
   - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 13992780 bp
       Num Contigs Represented = 40
       Non ambiguous bp:
             Initial: 13613654 bp
             After Masking: 11718563 bp
             Masked: 13.92 % 
 -- Input Database Coverage: 24171312 bp out of 24171523 bp ( 100.00 % )
Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 70500
Comparison Time: 00:18:41 (hh:mm:ss) Elapsed Time, 7894 HSPs Collected
Number of families returned by RECON: 1750
Round Time: 00:20:11 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 70 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.W2gYJK/RM_2364683.WedFeb111110092026
# 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: 00:00:11 (hh:mm:ss) Elapsed Time


Program Time: 00:36:56 (hh:mm:ss) Elapsed Time