RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.ELfRkI/RM_2866630.FriSep120024422025
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: 1757661882
Database = /dev/shm/rModeler.ELfRkI/GCA_029405315.1_ASM2940531v1 
  - Sequences = 10
  - Bases = 33203228
Storage Throughput = excellent ( 1646.30 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 33203103 bp ( 33203103 non ambiguous )
   - Num Contigs Represented = 10
   - 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.. : 386 raw families identified
   - RepeatScout: Running filtering stage.. 378 families remaining
   - RepeatScout: 00:01:11 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 368 families... 00:02:03 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 5 satellite(s), 153 contained, found in 00:00:03 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time
Round Time: 00:03:22 (hh:mm:ss) Elapsed Time : 210 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4637 repeats masked totaling 1631628 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10000389 bp
       Num Contigs Represented = 8
       Non ambiguous bp:
             Initial: 10000389 bp
             After Masking: 8304850 bp
             Masked: 16.95 % 
 -- Input Database Coverage: 10000389 bp out of 33203228 bp ( 30.12 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31626
Comparison Time: 00:03:21 (hh:mm:ss) Elapsed Time, 5554 HSPs Collected
Number of families returned by RECON: 1042
Round Time: 00:03:52 (hh:mm:ss) Elapsed Time : 12 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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       12520 repeats masked totaling 3668635 bp(s).
   - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 23202692 bp
       Num Contigs Represented = 10
       Non ambiguous bp:
             Initial: 23202692 bp
             After Masking: 19397084 bp
             Masked: 16.40 % 
 -- Input Database Coverage: 33203081 bp out of 33203228 bp ( 100.00 % )
Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 170236
Comparison Time: 00:09:44 (hh:mm:ss) Elapsed Time, 24552 HSPs Collected
Number of families returned by RECON: 2834
Round Time: 00:10:42 (hh:mm:ss) Elapsed Time : 42 families discovered.

RepeatScout/RECON discovery complete: 264 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.ELfRkI/RM_2866630.FriSep120024422025
# 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: 00:00:45 (hh:mm:ss) Elapsed Time


Program Time: 00:18:41 (hh:mm:ss) Elapsed Time