RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.nEM0Ji/RM_1663282.ThuSep112344572025
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: 1757659496
Database = /dev/shm/rModeler.nEM0Ji/GCA_028505765.1_ASM2850576v1 
  - Sequences = 61
  - Bases = 38711712
Storage Throughput = excellent ( 1085.27 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38711611 bp ( 38711611 non ambiguous )
   - Num Contigs Represented = 61
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 44 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:01:00 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 16 families... 00:00:11 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:21 (hh:mm:ss) Elapsed Time : 16 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 00:00:16 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       189 repeats masked totaling 43735 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10011219 bp
       Num Contigs Represented = 33
       Non ambiguous bp:
             Initial: 10011219 bp
             After Masking: 9950650 bp
             Masked: 0.61 % 
 -- Input Database Coverage: 10011219 bp out of 38711712 bp ( 25.86 % )
Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33411
Comparison Time: 00:12:41 (hh:mm:ss) Elapsed Time, 1725 HSPs Collected
Number of families returned by RECON: 715
Round Time: 00:13:11 (hh:mm:ss) Elapsed Time : 2 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:45 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       581 repeats masked totaling 106026 bp(s).
   - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28700312 bp
       Num Contigs Represented = 48
       Non ambiguous bp:
             Initial: 28700312 bp
             After Masking: 28548804 bp
             Masked: 0.53 % 
 -- Input Database Coverage: 38711531 bp out of 38711712 bp ( 100.00 % )
Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 280126
Comparison Time: 00:52:27 (hh:mm:ss) Elapsed Time, 14450 HSPs Collected
Number of families returned by RECON: 3511
Round Time: 01:51:31 (hh:mm:ss) Elapsed Time : 10 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.nEM0Ji/RM_1663282.ThuSep112344572025
# 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: 00:00:23 (hh:mm:ss) Elapsed Time


Program Time: 02:06:26 (hh:mm:ss) Elapsed Time