RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.WShyXR/RM_336659.MonSep81016122025
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: 1757351771
Database = /dev/shm/rModeler.WShyXR/GCA_000151005.2_ASM15100v2 
  - Sequences = 17
  - Bases = 37943219
Storage Throughput = excellent ( 1149.51 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37943186 bp ( 37689641 non ambiguous )
   - Num Contigs Represented = 17
   - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 107 raw families identified
   - RepeatScout: Running filtering stage.. 104 families remaining
   - RepeatScout: 00:05:46 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 103 families... 00:19:59 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 42 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time
Round Time: 00:26:01 (hh:mm:ss) Elapsed Time : 61 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (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...
       2212 repeats masked totaling 2877400 bp(s).
   - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10118996 bp
       Num Contigs Represented = 13
       Non ambiguous bp:
             Initial: 10001887 bp
             After Masking: 7096854 bp
             Masked: 29.04 % 
 -- Input Database Coverage: 10118996 bp out of 37943219 bp ( 26.67 % )
Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32640
Comparison Time: 00:04:47 (hh:mm:ss) Elapsed Time, 1771 HSPs Collected
Number of families returned by RECON: 408
Round Time: 00:05:29 (hh:mm:ss) Elapsed Time : 4 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:06 (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...
       6331 repeats masked totaling 8170572 bp(s).
   - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27824175 bp
       Num Contigs Represented = 16
       Non ambiguous bp:
             Initial: 27687739 bp
             After Masking: 19439073 bp
             Masked: 29.79 % 
 -- Input Database Coverage: 37943171 bp out of 37943219 bp ( 100.00 % )
Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 244650
Comparison Time: 00:21:17 (hh:mm:ss) Elapsed Time, 12480 HSPs Collected
Number of families returned by RECON: 1695
Round Time: 00:23:32 (hh:mm:ss) Elapsed Time : 26 families discovered.

RepeatScout/RECON discovery complete: 91 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.WShyXR/RM_336659.MonSep81016122025
# 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: 00:01:17 (hh:mm:ss) Elapsed Time


Program Time: 00:56:19 (hh:mm:ss) Elapsed Time