RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.Nav2gv/RM_364881.MonSep81152322025
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: 1757357551
Database = /dev/shm/rModeler.Nav2gv/GCA_000697725.1_RhiOry99-892-1.0 
  - Sequences = 1168
  - Bases = 39063757
  - N50 = 118148
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  470770-504351 |                                                   [ 2 ]
  437189-470769 |                                                   [ 1 ]
  403608-437188 |                                                   [ 3 ]
  370028-403608 |                                                   [ 2 ]
  336447-370027 |                                                   [ 3 ]
  302866-336446 |                                                   [ 7 ]
  269285-302865 |                                                   [ 6 ]
  235705-269285 |                                                   [ 6 ]
  202124-235704 |                                                   [ 9 ]
  168543-202123 |                                                   [ 14 ]
  134962-168542 |*                                                  [ 23 ]
  101382-134962 |**                                                 [ 48 ]
  67801-101381  |****                                               [ 75 ]
  34220-67800   |*****                                              [ 91 ]
  640-34220     |************************************************** [ 878 ]

Storage Throughput = excellent ( 1665.08 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39063657 bp ( 37463806 non ambiguous )
   - Num Contigs Represented = 1168
   - 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.. : 412 raw families identified
   - RepeatScout: Running filtering stage.. 402 families remaining
   - RepeatScout: 00:01:40 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 387 families... 00:00:43 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 84 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:02:29 (hh:mm:ss) Elapsed Time : 303 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 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4864 repeats masked totaling 1407354 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10465527 bp
       Num Contigs Represented = 398
       Non ambiguous bp:
             Initial: 10024044 bp
             After Masking: 8596161 bp
             Masked: 14.24 % 
 -- Input Database Coverage: 10465527 bp out of 39063757 bp ( 26.79 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 120295
Comparison Time: 00:06:16 (hh:mm:ss) Elapsed Time, 5249 HSPs Collected
Number of families returned by RECON: 1598
Round Time: 00:06:47 (hh:mm:ss) Elapsed Time : 4 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 00:00:24 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       13337 repeats masked totaling 3889604 bp(s).
   - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28598125 bp
       Num Contigs Represented = 926
       Non ambiguous bp:
             Initial: 27439757 bp
             After Masking: 23493100 bp
             Masked: 14.38 % 
 -- Input Database Coverage: 39063652 bp out of 39063757 bp ( 100.00 % )
Sampling Time: 00:00:46 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 957036
Comparison Time: 00:26:48 (hh:mm:ss) Elapsed Time, 33456 HSPs Collected
Number of families returned by RECON: 5987
Round Time: 00:28:09 (hh:mm:ss) Elapsed Time : 60 families discovered.

RepeatScout/RECON discovery complete: 367 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.Nav2gv/RM_364881.MonSep81152322025
# 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: 00:00:38 (hh:mm:ss) Elapsed Time


Program Time: 00:38:03 (hh:mm:ss) Elapsed Time