RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.9zrmYM/RM_2764781.WedSep101227002025
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: 1757532419
Database = /data/tmp/rModeler.9zrmYM/GCA_013145875.1_ASM1314587v1 
  - Sequences = 232
  - Bases = 39145403
  - N50 = 745634
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1771115-1897605 |                                                   [ 1 ]
  1644626-1771115 |                                                   [ 1 ]
  1518137-1644626 |                                                   [ 1 ]
  1391647-1518136 |                                                   [  ]
  1265158-1391647 |                                                   [ 3 ]
  1138669-1265158 |                                                   [ 1 ]
  1012180-1138669 |                                                   [ 2 ]
  885690-1012179  |*                                                  [ 4 ]
  759201-885690   |                                                   [ 3 ]
  632712-759201   |*                                                  [ 6 ]
  506223-632712   |*                                                  [ 6 ]
  379733-506222   |*                                                  [ 4 ]
  253244-379733   |*****                                              [ 17 ]
  126755-253244   |*****                                              [ 17 ]
  266-126755      |************************************************** [ 166 ]

Storage Throughput = good ( 939.58 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39145364 bp ( 39132171 non ambiguous )
   - Num Contigs Represented = 232
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 34 raw families identified
   - RepeatScout: Running filtering stage.. 16 families remaining
   - RepeatScout: 00:01:01 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 16 families... 00:00:18 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 1 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:26 (hh:mm:ss) Elapsed Time : 15 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       141 repeats masked totaling 38402 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10018998 bp
       Num Contigs Represented = 107
       Non ambiguous bp:
             Initial: 10015402 bp
             After Masking: 9960940 bp
             Masked: 0.54 % 
 -- Input Database Coverage: 10018998 bp out of 39145403 bp ( 25.59 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 43956
Comparison Time: 00:10:51 (hh:mm:ss) Elapsed Time, 1953 HSPs Collected
Number of families returned by RECON: 780
Round Time: 00:11:09 (hh:mm:ss) Elapsed Time : 0 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       433 repeats masked totaling 89351 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29126288 bp
       Num Contigs Represented = 192
       Non ambiguous bp:
             Initial: 29116691 bp
             After Masking: 28985859 bp
             Masked: 0.45 % 
 -- Input Database Coverage: 39145286 bp out of 39145403 bp ( 100.00 % )
Sampling Time: 00:00:46 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 363378
Comparison Time: 01:10:11 (hh:mm:ss) Elapsed Time, 17448 HSPs Collected
Number of families returned by RECON: 3657
Round Time: 03:45:56 (hh:mm:ss) Elapsed Time : 13 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.9zrmYM/RM_2764781.WedSep101227002025
# 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: 00:00:23 (hh:mm:ss) Elapsed Time


Program Time: 03:58:54 (hh:mm:ss) Elapsed Time