RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.oSMabj/RM_3563759.FriSep122006332025
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: 1757732793
Database = /dev/shm/rModeler.oSMabj/GCA_051397545.1_GA10_26 
  - Sequences = 168
  - Bases = 38524755
  - N50 = 1113531
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2301547-2465908 |                                                   [ 1 ]
  2137187-2301547 |                                                   [  ]
  1972827-2137187 |                                                   [  ]
  1808467-1972827 |                                                   [ 2 ]
  1644107-1808467 |                                                   [ 1 ]
  1479747-1644107 |*                                                  [ 3 ]
  1315387-1479747 |                                                   [ 2 ]
  1151026-1315386 |                                                   [ 1 ]
  986666-1151026  |*                                                  [ 4 ]
  822306-986666   |*                                                  [ 3 ]
  657946-822306   |*                                                  [ 3 ]
  493586-657946   |***                                                [ 8 ]
  329226-493586   |**                                                 [ 6 ]
  164866-329226   |*****                                              [ 13 ]
  506-164866      |************************************************** [ 121 ]

Storage Throughput = excellent ( 1569.65 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38524632 bp ( 38524405 non ambiguous )
   - Num Contigs Represented = 168
   - 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.. : 23 raw families identified
   - RepeatScout: Running filtering stage.. 21 families remaining
   - RepeatScout: 00:00:36 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 19 families... 00:00:09 (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: 00:00:50 (hh:mm:ss) Elapsed Time : 17 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:00 (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...
       177 repeats masked totaling 51319 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10000421 bp
       Num Contigs Represented = 85
       Non ambiguous bp:
             Initial: 10000360 bp
             After Masking: 9935072 bp
             Masked: 0.65 % 
 -- Input Database Coverage: 10000421 bp out of 38524755 bp ( 25.96 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 39903
Comparison Time: 00:03:39 (hh:mm:ss) Elapsed Time, 1627 HSPs Collected
Number of families returned by RECON: 718
Round Time: 00:03:51 (hh:mm:ss) Elapsed Time : 1 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       560 repeats masked totaling 140571 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28524138 bp
       Num Contigs Represented = 136
       Non ambiguous bp:
             Initial: 28523972 bp
             After Masking: 28340762 bp
             Masked: 0.64 % 
 -- Input Database Coverage: 38524559 bp out of 38524755 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 322003
Comparison Time: 00:14:11 (hh:mm:ss) Elapsed Time, 14287 HSPs Collected
Number of families returned by RECON: 3657
Round Time: 00:14:50 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 29 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.oSMabj/RM_3563759.FriSep122006332025
# 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: 00:19:38 (hh:mm:ss) Elapsed Time