RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.oXq8xC/RM_3483614.TueSep92350302025
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: 1757487029
Database = /dev/shm/rModeler.oXq8xC/GCA_013145995.1_ASM1314599v1 
  - Sequences = 78
  - Bases = 37767028
Storage Throughput = excellent ( 1687.03 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37766882 bp ( 37756854 non ambiguous )
   - Num Contigs Represented = 78
   - 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.. : 19 raw families identified
   - RepeatScout: Running filtering stage.. 13 families remaining
   - RepeatScout: 00:00:59 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 13 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 1 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:08 (hh:mm:ss) Elapsed Time : 12 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 00:00:18 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       129 repeats masked totaling 19973 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10017837 bp
       Num Contigs Represented = 54
       Non ambiguous bp:
             Initial: 10016022 bp
             After Masking: 9976076 bp
             Masked: 0.40 % 
 -- Input Database Coverage: 10017837 bp out of 37767028 bp ( 26.53 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33930
Comparison Time: 00:32:34 (hh:mm:ss) Elapsed Time, 1455 HSPs Collected
Number of families returned by RECON: 627
Round Time: 01:22:54 (hh:mm:ss) Elapsed Time : 0 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 00:00:43 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       389 repeats masked totaling 56327 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27748995 bp
       Num Contigs Represented = 75
       Non ambiguous bp:
             Initial: 27740782 bp
             After Masking: 27630115 bp
             Masked: 0.40 % 
 -- Input Database Coverage: 37766832 bp out of 37767028 bp ( 100.00 % )
Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 264628
Comparison Time: 01:19:10 (hh:mm:ss) Elapsed Time, 13019 HSPs Collected
Number of families returned by RECON: 3393
Round Time: 01:37:42 (hh:mm:ss) Elapsed Time : 10 families discovered.

RepeatScout/RECON discovery complete: 22 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.oXq8xC/RM_3483614.TueSep92350302025
# 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: 00:00:14 (hh:mm:ss) Elapsed Time


Program Time: 03:01:58 (hh:mm:ss) Elapsed Time