RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.O80m7c/RM_1936127.TueSep91817332025
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: 1757467053
Database = /dev/shm/rModeler.O80m7c/GCA_011763565.1_ASM1176356v1 
  - Sequences = 7164
  - Bases = 26442057
  - N50 = 32502
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  156182-167324 |                                                   [ 1 ]
  145040-156181 |                                                   [  ]
  133899-145040 |                                                   [ 1 ]
  122757-133898 |                                                   [ 2 ]
  111616-122757 |                                                   [ 5 ]
  100474-111615 |                                                   [ 9 ]
  89332-100473  |                                                   [ 5 ]
  78191-89332   |                                                   [ 11 ]
  67049-78190   |                                                   [ 20 ]
  55908-67049   |                                                   [ 31 ]
  44766-55907   |                                                   [ 59 ]
  33624-44765   |                                                   [ 75 ]
  22483-33624   |*                                                  [ 156 ]
  11341-22482   |**                                                 [ 268 ]
  200-11341     |************************************************** [ 6521 ]

Storage Throughput = excellent ( 1664.87 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 26441975 bp ( 26440524 non ambiguous )
   - Num Contigs Represented = 7164
   - 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.. : 257 raw families identified
   - RepeatScout: Running filtering stage.. 253 families remaining
   - RepeatScout: 00:00:54 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 242 families... 00:00:27 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 61 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:01:27 (hh:mm:ss) Elapsed Time : 181 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 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3810 repeats masked totaling 962885 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10001206 bp
       Num Contigs Represented = 2746
       Non ambiguous bp:
             Initial: 10000602 bp
             After Masking: 9008655 bp
             Masked: 9.92 % 
 -- Input Database Coverage: 10001206 bp out of 26442057 bp ( 37.82 % )
Sampling Time: 00:00:14 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 3857253
Comparison Time: 00:12:35 (hh:mm:ss) Elapsed Time, 17074 HSPs Collected
Number of families returned by RECON: 2079
Round Time: 00:13:01 (hh:mm:ss) Elapsed Time : 10 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       7089 repeats masked totaling 1724786 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 16440737 bp
       Num Contigs Represented = 4507
       Non ambiguous bp:
             Initial: 16439890 bp
             After Masking: 14664775 bp
             Masked: 10.80 % 
 -- Input Database Coverage: 26441943 bp out of 26442057 bp ( 100.00 % )
Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 10550121
Comparison Time: 00:22:13 (hh:mm:ss) Elapsed Time, 17610 HSPs Collected
Number of families returned by RECON: 4121
Round Time: 00:23:11 (hh:mm:ss) Elapsed Time : 21 families discovered.

RepeatScout/RECON discovery complete: 212 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.O80m7c/RM_1936127.TueSep91817332025
# 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: 00:00:21 (hh:mm:ss) Elapsed Time


Program Time: 00:38:00 (hh:mm:ss) Elapsed Time