RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.a7gTyf/RM_4054516.TueSep91739302025
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: 1757464769
Database = /dev/shm/rModeler.a7gTyf/GCA_011762625.1_ASM1176262v1 
  - Sequences = 3625
  - Bases = 25405152
  - N50 = 36400
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  227439-243671 |                                                   [ 1 ]
  211208-227439 |                                                   [  ]
  194976-211207 |                                                   [ 1 ]
  178745-194976 |                                                   [  ]
  162514-178745 |                                                   [ 2 ]
  146282-162513 |                                                   [  ]
  130051-146282 |                                                   [ 1 ]
  113819-130050 |                                                   [ 4 ]
  97588-113819  |                                                   [ 10 ]
  81357-97588   |                                                   [ 13 ]
  65125-81356   |                                                   [ 34 ]
  48894-65125   |                                                   [ 62 ]
  32662-48893   |*                                                  [ 118 ]
  16431-32662   |***                                                [ 236 ]
  200-16431     |************************************************** [ 3143 ]

Storage Throughput = excellent ( 1123.54 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 25405080 bp ( 25403066 non ambiguous )
   - Num Contigs Represented = 3625
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 259 raw families identified
   - RepeatScout: Running filtering stage.. 255 families remaining
   - RepeatScout: 00:02:05 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 246 families... 00:00:43 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 57 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:02:58 (hh:mm:ss) Elapsed Time : 189 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3863 repeats masked totaling 989710 bp(s).
   - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10040050 bp
       Num Contigs Represented = 1443
       Non ambiguous bp:
             Initial: 10039346 bp
             After Masking: 9018659 bp
             Masked: 10.17 % 
 -- Input Database Coverage: 10040050 bp out of 25405152 bp ( 39.52 % )
Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1090026
Comparison Time: 00:12:29 (hh:mm:ss) Elapsed Time, 19726 HSPs Collected
Number of families returned by RECON: 1988
Round Time: 00:13:28 (hh:mm:ss) Elapsed Time : 14 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 00:00:24 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6858 repeats masked totaling 1676125 bp(s).
   - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 15364950 bp
       Num Contigs Represented = 2283
       Non ambiguous bp:
             Initial: 15363640 bp
             After Masking: 13643238 bp
             Masked: 11.20 % 
 -- Input Database Coverage: 25405000 bp out of 25405152 bp ( 100.00 % )
Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2814378
Comparison Time: 00:22:38 (hh:mm:ss) Elapsed Time, 13653 HSPs Collected
Number of families returned by RECON: 3264
Round Time: 00:24:07 (hh:mm:ss) Elapsed Time : 22 families discovered.

RepeatScout/RECON discovery complete: 225 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.a7gTyf/RM_4054516.TueSep91739302025
# 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: 00:01:01 (hh:mm:ss) Elapsed Time


Program Time: 00:41:34 (hh:mm:ss) Elapsed Time