RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.cfLD9S/RM_216585.WedSep101426232025
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: 1757539583
Database = /dev/shm/rModeler.cfLD9S/GCA_018154645.1_ASM1815464v1 
  - Sequences = 319
  - Bases = 19573542
  - N50 = 446739
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1592276-1705996 |                                                   [ 1 ]
  1478556-1592275 |                                                   [ 1 ]
  1364836-1478555 |                                                   [  ]
  1251117-1364836 |                                                   [  ]
  1137397-1251116 |                                                   [  ]
  1023677-1137396 |                                                   [  ]
  909957-1023676  |                                                   [  ]
  796238-909957   |                                                   [  ]
  682518-796237   |                                                   [ 1 ]
  568798-682517   |                                                   [ 2 ]
  455078-568797   |*                                                  [ 8 ]
  341359-455078   |*                                                  [ 7 ]
  227639-341358   |**                                                 [ 14 ]
  113919-227638   |***                                                [ 17 ]
  200-113919      |************************************************** [ 268 ]

Storage Throughput = excellent ( 1684.60 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19573483 bp ( 19564322 non ambiguous )
   - Num Contigs Represented = 319
   - 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.. : 27 raw families identified
   - RepeatScout: Running filtering stage.. 26 families remaining
   - RepeatScout: 00:00:26 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 24 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 6 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:35 (hh:mm:ss) Elapsed Time : 18 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       285 repeats masked totaling 48259 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10016089 bp
       Num Contigs Represented = 198
       Non ambiguous bp:
             Initial: 10011100 bp
             After Masking: 9906944 bp
             Masked: 1.04 % 
 -- Input Database Coverage: 10016089 bp out of 19573542 bp ( 51.17 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 78606
Comparison Time: 00:04:37 (hh:mm:ss) Elapsed Time, 17180 HSPs Collected
Number of families returned by RECON: 1525
Round Time: 00:05:10 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 39573542


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39573542 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...
       1864 repeats masked totaling 178352 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9557369 bp
       Num Contigs Represented = 175
       Non ambiguous bp:
             Initial: 9553197 bp
             After Masking: 9325501 bp
             Masked: 2.38 % 
 -- Input Database Coverage: 19573458 bp out of 19573542 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 67896
Comparison Time: 00:04:19 (hh:mm:ss) Elapsed Time, 2585 HSPs Collected
Number of families returned by RECON: 851
Round Time: 00:04:39 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 23 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.cfLD9S/RM_216585.WedSep101426232025
# 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: 00:10:29 (hh:mm:ss) Elapsed Time