RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.bWM7OA/RM_3951223.MonSep81100142025
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: 1757354413
Database = /dev/shm/rModeler.bWM7OA/GCA_000417875.1_Pflocc_1.0 
  - Sequences = 39
  - Bases = 23305380
Storage Throughput = excellent ( 1665.97 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 23305241 bp ( 22963041 non ambiguous )
   - Num Contigs Represented = 39
   - 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.. : 32 raw families identified
   - RepeatScout: Running filtering stage.. 29 families remaining
   - RepeatScout: 00:01:07 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 29 families... 00:00:16 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 6 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:26 (hh:mm:ss) Elapsed Time : 23 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       403 repeats masked totaling 69368 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10146135 bp
       Num Contigs Represented = 34
       Non ambiguous bp:
             Initial: 10005118 bp
             After Masking: 9834991 bp
             Masked: 1.70 % 
 -- Input Database Coverage: 10146135 bp out of 23305380 bp ( 43.54 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 34980
Comparison Time: 00:07:43 (hh:mm:ss) Elapsed Time, 2818 HSPs Collected
Number of families returned by RECON: 1031
Round Time: 00:08:11 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 43305380


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 43305380 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...
       1209 repeats masked totaling 173525 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 13159070 bp
       Num Contigs Represented = 34
       Non ambiguous bp:
             Initial: 12957887 bp
             After Masking: 12663595 bp
             Masked: 2.27 % 
 -- Input Database Coverage: 23305205 bp out of 23305380 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 56616
Comparison Time: 00:10:27 (hh:mm:ss) Elapsed Time, 3314 HSPs Collected
Number of families returned by RECON: 1489
Round Time: 00:11:25 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.bWM7OA/RM_3951223.MonSep81100142025
# 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: 00:00:07 (hh:mm:ss) Elapsed Time


Program Time: 00:21:09 (hh:mm:ss) Elapsed Time