RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.F6ufFp/RM_897513.MonSep81249042025
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: 1757360943
Database = /dev/shm/rModeler.F6ufFp/GCA_000875795.1_Cryp_gatt_CA1014_V1 
  - Sequences = 21
  - Bases = 17527606
Storage Throughput = excellent ( 1669.96 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 17527464 bp ( 17394579 non ambiguous )
   - Num Contigs Represented = 21
   - 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.. : 18 raw families identified
   - RepeatScout: Running filtering stage.. 16 families remaining
   - RepeatScout: 00:00:14 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 16 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:21 (hh:mm:ss) Elapsed Time : 14 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...
       227 repeats masked totaling 54768 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10047815 bp
       Num Contigs Represented = 21
       Non ambiguous bp:
             Initial: 10006669 bp
             After Masking: 9942688 bp
             Masked: 0.64 % 
 -- Input Database Coverage: 10047815 bp out of 17527606 bp ( 57.33 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32131
Comparison Time: 00:03:28 (hh:mm:ss) Elapsed Time, 1593 HSPs Collected
Number of families returned by RECON: 585
Round Time: 00:03:39 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 37527606


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 37527606 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       221 repeats masked totaling 54761 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 7479569 bp
       Num Contigs Represented = 21
       Non ambiguous bp:
             Initial: 7387830 bp
             After Masking: 7323926 bp
             Masked: 0.86 % 
 -- Input Database Coverage: 17527384 bp out of 17527606 bp ( 100.00 % )
Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 18721
Comparison Time: 00:02:33 (hh:mm:ss) Elapsed Time, 934 HSPs Collected
Number of families returned by RECON: 335
Round Time: 00:02:41 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 15 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.F6ufFp/RM_897513.MonSep81249042025
# 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: 00:06:47 (hh:mm:ss) Elapsed Time