RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.2ljtfL/RM_1702287.FriSep122053262025
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: 1757735606
Database = /dev/shm/rModeler.2ljtfL/GCA_051527495.1_YNP34 
  - Sequences = 1346
  - Bases = 30369633
  - N50 = 44192
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  234477-251158 |                                                   [ 1 ]
  217797-234477 |                                                   [ 1 ]
  201116-217796 |                                                   [ 1 ]
  184436-201116 |                                                   [  ]
  167755-184435 |                                                   [ 3 ]
  151075-167755 |                                                   [ 2 ]
  134394-151074 |                                                   [ 8 ]
  117714-134394 |                                                   [ 8 ]
  101033-117713 |                                                   [ 9 ]
  84353-101033  |*                                                  [ 20 ]
  67672-84352   |**                                                 [ 42 ]
  50992-67672   |***                                                [ 59 ]
  34311-50991   |*******                                            [ 117 ]
  17631-34311   |****************                                   [ 271 ]
  951-17631     |************************************************** [ 804 ]

Storage Throughput = excellent ( 1688.07 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 30369589 bp ( 30362056 non ambiguous )
   - Num Contigs Represented = 1346
   - 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.. : 177 raw families identified
   - RepeatScout: Running filtering stage.. 173 families remaining
   - RepeatScout: 00:00:47 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 163 families... 00:00:24 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 37 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:16 (hh:mm:ss) Elapsed Time : 126 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2460 repeats masked totaling 644078 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10029076 bp
       Num Contigs Represented = 507
       Non ambiguous bp:
             Initial: 10026673 bp
             After Masking: 9345869 bp
             Masked: 6.79 % 
 -- Input Database Coverage: 10029076 bp out of 30369633 bp ( 33.02 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 147696
Comparison Time: 00:05:03 (hh:mm:ss) Elapsed Time, 10877 HSPs Collected
Number of families returned by RECON: 1543
Round Time: 00:05:28 (hh:mm:ss) Elapsed Time : 18 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...
       7274 repeats masked totaling 1446942 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 20340455 bp
       Num Contigs Represented = 975
       Non ambiguous bp:
             Initial: 20335325 bp
             After Masking: 18807811 bp
             Masked: 7.51 % 
 -- Input Database Coverage: 30369531 bp out of 30369633 bp ( 100.00 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 637885
Comparison Time: 00:11:40 (hh:mm:ss) Elapsed Time, 24596 HSPs Collected
Number of families returned by RECON: 3094
Round Time: 00:12:29 (hh:mm:ss) Elapsed Time : 41 families discovered.

RepeatScout/RECON discovery complete: 185 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.2ljtfL/RM_1702287.FriSep122053262025
# 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: 00:00:17 (hh:mm:ss) Elapsed Time


Program Time: 00:19:30 (hh:mm:ss) Elapsed Time