RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.HA6Yyu/RM_3497901.ThuSep110153572025
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: 1757580836
Database = /data/tmp/rModeler.HA6Yyu/GCA_022288665.1_ASM2228866v1 
  - Sequences = 1440
  - Bases = 30117611
  - N50 = 42002
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  196654-210630 |                                                   [ 1 ]
  182679-196654 |                                                   [  ]
  168704-182679 |                                                   [ 1 ]
  154729-168704 |                                                   [ 3 ]
  140754-154729 |                                                   [ 6 ]
  126778-140753 |                                                   [ 4 ]
  112803-126778 |                                                   [ 4 ]
  98828-112803  |                                                   [ 7 ]
  84853-98828   |*                                                  [ 21 ]
  70878-84853   |*                                                  [ 30 ]
  56902-70877   |**                                                 [ 43 ]
  42927-56902   |*****                                              [ 86 ]
  28952-42927   |********                                           [ 139 ]
  14977-28952   |****************                                   [ 269 ]
  1002-14977    |************************************************** [ 826 ]

Storage Throughput = excellent ( 1513.50 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 30117512 bp ( 30111361 non ambiguous )
   - Num Contigs Represented = 1440
   - 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.. : 124 raw families identified
   - RepeatScout: Running filtering stage.. 122 families remaining
   - RepeatScout: 00:01:18 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 116 families... 00:00:23 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 28 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:47 (hh:mm:ss) Elapsed Time : 88 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 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1935 repeats masked totaling 585692 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10022379 bp
       Num Contigs Represented = 547
       Non ambiguous bp:
             Initial: 10020395 bp
             After Masking: 9398165 bp
             Masked: 6.21 % 
 -- Input Database Coverage: 10022379 bp out of 30117611 bp ( 33.28 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 173166
Comparison Time: 00:06:29 (hh:mm:ss) Elapsed Time, 10989 HSPs Collected
Number of families returned by RECON: 1527
Round Time: 00:07:02 (hh:mm:ss) Elapsed Time : 21 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 00:00:22 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6155 repeats masked totaling 1177201 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 20095116 bp
       Num Contigs Represented = 1003
       Non ambiguous bp:
             Initial: 20090949 bp
             After Masking: 18842362 bp
             Masked: 6.21 % 
 -- Input Database Coverage: 30117495 bp out of 30117611 bp ( 100.00 % )
Sampling Time: 00:00:34 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 661825
Comparison Time: 00:16:23 (hh:mm:ss) Elapsed Time, 30246 HSPs Collected
Number of families returned by RECON: 3304
Round Time: 00:17:53 (hh:mm:ss) Elapsed Time : 62 families discovered.

RepeatScout/RECON discovery complete: 171 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.HA6Yyu/RM_3497901.ThuSep110153572025
# 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: 00:00:29 (hh:mm:ss) Elapsed Time


Program Time: 00:27:11 (hh:mm:ss) Elapsed Time