RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.MtMqDg/RM_1575218.WedFeb111122422026
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: 1770837761
Database = /dev/shm/rModeler.MtMqDg/GCA_023845515.1_StPkA1H1 
  - Sequences = 73
  - Bases = 24311409
Storage Throughput = excellent ( 1633.70 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 24311312 bp ( 24101846 non ambiguous )
   - Num Contigs Represented = 73
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 148 raw families identified
   - RepeatScout: Running filtering stage.. 60 families remaining
   - RepeatScout: 00:01:34 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 59 families... 00:00:52 (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: 00:02:30 (hh:mm:ss) Elapsed Time : 41 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2918 repeats masked totaling 503431 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10111849 bp
       Num Contigs Represented = 41
       Non ambiguous bp:
             Initial: 10022251 bp
             After Masking: 8721818 bp
             Masked: 12.98 % 
 -- Input Database Coverage: 10111849 bp out of 24311409 bp ( 41.59 % )
Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 38226
Comparison Time: 00:14:18 (hh:mm:ss) Elapsed Time, 14243 HSPs Collected
Number of families returned by RECON: 1425
Round Time: 00:15:54 (hh:mm:ss) Elapsed Time : 12 families discovered.
   - Increasing sample size to include end piece now = 44311409


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 44311409 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5198 repeats masked totaling 917567 bp(s).
   - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 14199451 bp
       Num Contigs Represented = 46
       Non ambiguous bp:
             Initial: 14079583 bp
             After Masking: 11989909 bp
             Masked: 14.84 % 
 -- Input Database Coverage: 24311300 bp out of 24311409 bp ( 100.00 % )
Sampling Time: 00:01:33 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 75078
Comparison Time: 00:21:48 (hh:mm:ss) Elapsed Time, 9450 HSPs Collected
Number of families returned by RECON: 1988
Round Time: 00:23:35 (hh:mm:ss) Elapsed Time : 7 families discovered.

RepeatScout/RECON discovery complete: 60 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.MtMqDg/RM_1575218.WedFeb111122422026
# 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: 00:00:12 (hh:mm:ss) Elapsed Time


Program Time: 00:42:11 (hh:mm:ss) Elapsed Time