RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.W7sx0x/RM_2152944.WedSep101751422025
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: 1757551902
Database = /dev/shm/rModeler.W7sx0x/GCA_019054775.1_ASM1905477v1 
  - Sequences = 95
  - Bases = 39071468
Storage Throughput = excellent ( 1648.25 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39071386 bp ( 39071367 non ambiguous )
   - Num Contigs Represented = 95
   - 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.. : 24 raw families identified
   - RepeatScout: Running filtering stage.. 24 families remaining
   - RepeatScout: 00:00:41 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 22 families... 00:00:09 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 3 contained, found in 00:00:00 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:00 (hh:mm:ss) Elapsed Time
Round Time: 00:00:54 (hh:mm:ss) Elapsed Time : 19 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       179 repeats masked totaling 56657 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10022561 bp
       Num Contigs Represented = 58
       Non ambiguous bp:
             Initial: 10022561 bp
             After Masking: 9948607 bp
             Masked: 0.74 % 
 -- Input Database Coverage: 10022561 bp out of 39071468 bp ( 25.65 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33670
Comparison Time: 00:03:48 (hh:mm:ss) Elapsed Time, 45840 HSPs Collected
Number of families returned by RECON: 961
Round Time: 00:04:06 (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 : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       757 repeats masked totaling 159535 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29048745 bp
       Num Contigs Represented = 87
       Non ambiguous bp:
             Initial: 29048726 bp
             After Masking: 28855177 bp
             Masked: 0.67 % 
 -- Input Database Coverage: 39071306 bp out of 39071468 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 291466
Comparison Time: 00:15:17 (hh:mm:ss) Elapsed Time, 356634 HSPs Collected
Number of families returned by RECON: 4338
Round Time: 00:17:10 (hh:mm:ss) Elapsed Time : 5 families discovered.

RepeatScout/RECON discovery complete: 27 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.W7sx0x/RM_2152944.WedSep101751422025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:22:16 (hh:mm:ss) Elapsed Time