RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.eNyfUU/RM_3835325.TueFeb101335402026
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: 1770759339
Database = /dev/shm/rModeler.eNyfUU/GCA_900537975.2_LBRM_annotationDEFINITIVO 
  - Sequences = 35
  - Bases = 32380552
Storage Throughput = excellent ( 1684.64 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 32380423 bp ( 32380423 non ambiguous )
   - Num Contigs Represented = 35
   - 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.. : 164 raw families identified
   - RepeatScout: Running filtering stage.. 153 families remaining
   - RepeatScout: 00:01:44 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 135 families... 12:20:35 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 30 satellite(s), 24 contained, found in 00:00:27 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:27 (hh:mm:ss) Elapsed Time
Round Time: 12:22:49 (hh:mm:ss) Elapsed Time : 81 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 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2682 repeats masked totaling 678189 bp(s).
   - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10035247 bp
       Num Contigs Represented = 35
       Non ambiguous bp:
             Initial: 10035247 bp
             After Masking: 9269909 bp
             Masked: 7.63 % 
 -- Input Database Coverage: 10035247 bp out of 32380552 bp ( 30.99 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33670
Comparison Time: 00:04:01 (hh:mm:ss) Elapsed Time, 2862 HSPs Collected
Number of families returned by RECON: 726
Round Time: 00:04:26 (hh:mm:ss) Elapsed Time : 5 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 00:00:20 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6215 repeats masked totaling 1779831 bp(s).
   - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 22345118 bp
       Num Contigs Represented = 35
       Non ambiguous bp:
             Initial: 22345118 bp
             After Masking: 20338751 bp
             Masked: 8.98 % 
 -- Input Database Coverage: 32380365 bp out of 32380552 bp ( 100.00 % )
Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 161596
Comparison Time: 00:12:25 (hh:mm:ss) Elapsed Time, 10180 HSPs Collected
Number of families returned by RECON: 2478
Round Time: 00:13:19 (hh:mm:ss) Elapsed Time : 16 families discovered.

RepeatScout/RECON discovery complete: 102 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.eNyfUU/RM_3835325.TueFeb101335402026
# 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: 00:00:21 (hh:mm:ss) Elapsed Time


Program Time: 12:40:55 (hh:mm:ss) Elapsed Time