RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.8ROXFi/RM_1588936.FriSep122047572025
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: 1757735277
Database = /dev/shm/rModeler.8ROXFi/GCA_051527455.1_YNP36 
  - Sequences = 1348
  - Bases = 29924749
  - N50 = 43046
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  184453-197557 |                                                   [ 1 ]
  171349-184452 |                                                   [ 2 ]
  158245-171348 |                                                   [ 2 ]
  145142-158245 |                                                   [ 4 ]
  132038-145141 |                                                   [ 4 ]
  118934-132037 |                                                   [ 5 ]
  105830-118933 |                                                   [ 5 ]
  92727-105830  |                                                   [ 12 ]
  79623-92726   |*                                                  [ 22 ]
  66519-79622   |**                                                 [ 32 ]
  53415-66518   |***                                                [ 50 ]
  40312-53415   |******                                             [ 97 ]
  27208-40311   |**********                                         [ 148 ]
  14104-27207   |*****************                                  [ 251 ]
  1001-14104    |************************************************** [ 713 ]

Storage Throughput = excellent ( 1776.96 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 29924679 bp ( 29916815 non ambiguous )
   - Num Contigs Represented = 1348
   - 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.. : 180 raw families identified
   - RepeatScout: Running filtering stage.. 179 families remaining
   - RepeatScout: 00:00:46 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 168 families... 00:00:23 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 50 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:14 (hh:mm:ss) Elapsed Time : 118 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...
       2415 repeats masked totaling 659292 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10009350 bp
       Num Contigs Represented = 503
       Non ambiguous bp:
             Initial: 10007387 bp
             After Masking: 9314409 bp
             Masked: 6.92 % 
 -- Input Database Coverage: 10009350 bp out of 29924749 bp ( 33.45 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 152628
Comparison Time: 00:05:00 (hh:mm:ss) Elapsed Time, 10902 HSPs Collected
Number of families returned by RECON: 1552
Round Time: 00:05:29 (hh:mm:ss) Elapsed Time : 19 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6805 repeats masked totaling 1466182 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 19915249 bp
       Num Contigs Represented = 954
       Non ambiguous bp:
             Initial: 19909348 bp
             After Masking: 18355579 bp
             Masked: 7.80 % 
 -- Input Database Coverage: 29924599 bp out of 29924749 bp ( 100.00 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 617716
Comparison Time: 00:11:17 (hh:mm:ss) Elapsed Time, 25896 HSPs Collected
Number of families returned by RECON: 2993
Round Time: 00:12:06 (hh:mm:ss) Elapsed Time : 50 families discovered.

RepeatScout/RECON discovery complete: 187 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.8ROXFi/RM_1588936.FriSep122047572025
# 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: 00:00:16 (hh:mm:ss) Elapsed Time


Program Time: 00:19:05 (hh:mm:ss) Elapsed Time