RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.SKodjH/RM_2624197.FriSep122221002025
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: 1757740859
Database = /dev/shm/rModeler.SKodjH/GCA_051943695.1_ASM5194369v1 
  - Sequences = 1244
  - Bases = 22494273
  - N50 = 51400
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  168075-180067 |                                                   [ 4 ]
  156084-168075 |                                                   [ 1 ]
  144093-156084 |                                                   [ 1 ]
  132102-144093 |                                                   [ 8 ]
  120111-132102 |                                                   [ 7 ]
  108120-120111 |                                                   [ 3 ]
  96129-108120  |                                                   [ 6 ]
  84138-96129   |                                                   [ 15 ]
  72147-84138   |*                                                  [ 25 ]
  60156-72147   |**                                                 [ 33 ]
  48165-60156   |***                                                [ 51 ]
  36174-48165   |****                                               [ 75 ]
  24183-36174   |******                                             [ 96 ]
  12192-24183   |**********                                         [ 154 ]
  201-12192     |************************************************** [ 765 ]

Storage Throughput = excellent ( 1648.79 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 22494176 bp ( 22492287 non ambiguous )
   - Num Contigs Represented = 1244
   - 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.. : 15 raw families identified
   - RepeatScout: Running filtering stage.. 15 families remaining
   - RepeatScout: 00:00:23 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 15 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:30 (hh:mm:ss) Elapsed Time : 15 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...
       169 repeats masked totaling 40275 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10028265 bp
       Num Contigs Represented = 617
       Non ambiguous bp:
             Initial: 10027131 bp
             After Masking: 9945411 bp
             Masked: 0.81 % 
 -- Input Database Coverage: 10028265 bp out of 22494273 bp ( 44.58 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 233586
Comparison Time: 00:05:15 (hh:mm:ss) Elapsed Time, 1900 HSPs Collected
Number of families returned by RECON: 716
Round Time: 00:05:28 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 42494273


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 42494273 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       196 repeats masked totaling 50608 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 12465859 bp
       Num Contigs Represented = 733
       Non ambiguous bp:
             Initial: 12465104 bp
             After Masking: 12369084 bp
             Masked: 0.77 % 
 -- Input Database Coverage: 22494124 bp out of 22494273 bp ( 100.00 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 345696
Comparison Time: 00:06:36 (hh:mm:ss) Elapsed Time, 2501 HSPs Collected
Number of families returned by RECON: 954
Round Time: 00:06:54 (hh:mm:ss) Elapsed Time : 4 families discovered.

RepeatScout/RECON discovery complete: 20 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.SKodjH/RM_2624197.FriSep122221002025
# 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: 00:00:05 (hh:mm:ss) Elapsed Time


Program Time: 00:12:57 (hh:mm:ss) Elapsed Time