RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.09hi8f/RM_2356671.ThuSep110737152025
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: 1757601434
Database = /dev/shm/rModeler.09hi8f/GCA_023629935.1_ASM2362993v1 
  - Sequences = 832
  - Bases = 35418858
  - N50 = 103178
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  469406-502900 |                                                   [ 2 ]
  435913-469406 |                                                   [  ]
  402420-435913 |                                                   [  ]
  368927-402420 |                                                   [  ]
  335434-368927 |                                                   [  ]
  301940-335433 |                                                   [ 1 ]
  268447-301940 |                                                   [ 2 ]
  234954-268447 |                                                   [ 6 ]
  201461-234954 |                                                   [ 8 ]
  167968-201461 |*                                                  [ 17 ]
  134474-167967 |**                                                 [ 24 ]
  100981-134474 |*****                                              [ 54 ]
  67488-100981  |********                                           [ 90 ]
  33995-67488   |************                                       [ 123 ]
  502-33995     |************************************************** [ 505 ]

Storage Throughput = excellent ( 1703.96 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 35418824 bp ( 35406394 non ambiguous )
   - Num Contigs Represented = 832
   - 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.. : 181 raw families identified
   - RepeatScout: Running filtering stage.. 178 families remaining
   - RepeatScout: 00:01:16 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 169 families... 00:02:01 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 2 satellite(s), 39 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:03:21 (hh:mm:ss) Elapsed Time : 128 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...
       3341 repeats masked totaling 1182716 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10024148 bp
       Num Contigs Represented = 306
       Non ambiguous bp:
             Initial: 10022219 bp
             After Masking: 8808481 bp
             Masked: 12.11 % 
 -- Input Database Coverage: 10024148 bp out of 35418858 bp ( 28.30 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 75078
Comparison Time: 00:04:24 (hh:mm:ss) Elapsed Time, 3995 HSPs Collected
Number of families returned by RECON: 1463
Round Time: 00:04:41 (hh:mm:ss) Elapsed Time : 3 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 00:00:16 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       8813 repeats masked totaling 3001982 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 25394596 bp
       Num Contigs Represented = 691
       Non ambiguous bp:
             Initial: 25384095 bp
             After Masking: 22269960 bp
             Masked: 12.27 % 
 -- Input Database Coverage: 35418744 bp out of 35418858 bp ( 100.00 % )
Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 582660
Comparison Time: 00:15:09 (hh:mm:ss) Elapsed Time, 26508 HSPs Collected
Number of families returned by RECON: 5448
Round Time: 00:16:10 (hh:mm:ss) Elapsed Time : 12 families discovered.

RepeatScout/RECON discovery complete: 143 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.09hi8f/RM_2356671.ThuSep110737152025
# 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: 00:00:18 (hh:mm:ss) Elapsed Time


Program Time: 00:24:30 (hh:mm:ss) Elapsed Time