RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.p3sB4g/RM_3286197.FriSep120507412025
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: 1757678861
Database = /dev/shm/rModeler.p3sB4g/GCA_037042095.1_ASM3704209v1 
  - Sequences = 1417
  - Bases = 35147663
  - N50 = 73200
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  262935-281681 |                                                   [ 2 ]
  244190-262935 |                                                   [  ]
  225444-244189 |                                                   [  ]
  206699-225444 |                                                   [  ]
  187954-206699 |                                                   [ 6 ]
  169208-187953 |                                                   [ 6 ]
  150463-169208 |                                                   [ 6 ]
  131717-150462 |                                                   [ 9 ]
  112972-131717 |*                                                  [ 20 ]
  94227-112972  |**                                                 [ 43 ]
  75481-94226   |***                                                [ 56 ]
  56736-75481   |****                                               [ 77 ]
  37990-56735   |******                                             [ 126 ]
  19245-37990   |********                                           [ 154 ]
  500-19245     |************************************************** [ 912 ]

Storage Throughput = excellent ( 1475.40 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 35147568 bp ( 35147378 non ambiguous )
   - Num Contigs Represented = 1417
   - 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.. : 157 raw families identified
   - RepeatScout: Running filtering stage.. 154 families remaining
   - RepeatScout: 00:01:14 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 150 families... 00:01:10 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 satellite(s), 38 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:02:29 (hh:mm:ss) Elapsed Time : 111 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...
       2948 repeats masked totaling 1024646 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10026197 bp
       Num Contigs Represented = 480
       Non ambiguous bp:
             Initial: 10026171 bp
             After Masking: 8964527 bp
             Masked: 10.59 % 
 -- Input Database Coverage: 10026197 bp out of 35147663 bp ( 28.53 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 138601
Comparison Time: 00:05:02 (hh:mm:ss) Elapsed Time, 4475 HSPs Collected
Number of families returned by RECON: 1542
Round Time: 00:05:18 (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 : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       8200 repeats masked totaling 2844433 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 25121291 bp
       Num Contigs Represented = 1109
       Non ambiguous bp:
             Initial: 25121127 bp
             After Masking: 22187341 bp
             Masked: 11.68 % 
 -- Input Database Coverage: 35147488 bp out of 35147663 bp ( 100.00 % )
Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1000405
Comparison Time: 00:15:40 (hh:mm:ss) Elapsed Time, 27274 HSPs Collected
Number of families returned by RECON: 5673
Round Time: 00:16:43 (hh:mm:ss) Elapsed Time : 23 families discovered.

RepeatScout/RECON discovery complete: 136 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.p3sB4g/RM_3286197.FriSep120507412025
# 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: 00:00:17 (hh:mm:ss) Elapsed Time


Program Time: 00:24:47 (hh:mm:ss) Elapsed Time