RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.qgnAGq/RM_4170205.TueSep90454062025
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: 1757418846
Database = /dev/shm/rModeler.qgnAGq/GCA_006942295.1_Fgr0078 
  - Sequences = 335
  - Bases = 36775743
  - N50 = 714255
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1843996-1975695 |                                                   [ 1 ]
  1712298-1843996 |                                                   [ 1 ]
  1580600-1712298 |                                                   [  ]
  1448902-1580600 |                                                   [ 2 ]
  1317204-1448902 |                                                   [ 1 ]
  1185506-1317204 |                                                   [ 1 ]
  1053808-1185506 |                                                   [ 1 ]
  922110-1053808  |                                                   [ 2 ]
  790412-922110   |                                                   [ 4 ]
  658714-790412   |                                                   [ 4 ]
  527016-658714   |*                                                  [ 7 ]
  395318-527016   |*                                                  [ 7 ]
  263620-395318   |**                                                 [ 12 ]
  131922-263620   |***                                                [ 20 ]
  224-131922      |*************************************************  [ 272 ]

Storage Throughput = excellent ( 1655.16 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36775670 bp ( 36774712 non ambiguous )
   - Num Contigs Represented = 335
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 20 raw families identified
   - RepeatScout: Running filtering stage.. 20 families remaining
   - RepeatScout: 00:00:37 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 19 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:45 (hh:mm:ss) Elapsed Time : 17 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...
       172 repeats masked totaling 22816 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10012049 bp
       Num Contigs Represented = 143
       Non ambiguous bp:
             Initial: 10011806 bp
             After Masking: 9973040 bp
             Masked: 0.39 % 
 -- Input Database Coverage: 10012049 bp out of 36775743 bp ( 27.22 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 52975
Comparison Time: 00:04:06 (hh:mm:ss) Elapsed Time, 32301 HSPs Collected
Number of families returned by RECON: 910
Round Time: 00:04:23 (hh:mm:ss) Elapsed Time : 1 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...
       469 repeats masked totaling 69524 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26763548 bp
       Num Contigs Represented = 266
       Non ambiguous bp:
             Initial: 26762833 bp
             After Masking: 26650528 bp
             Masked: 0.42 % 
 -- Input Database Coverage: 36775597 bp out of 36775743 bp ( 100.00 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 371953
Comparison Time: 00:14:40 (hh:mm:ss) Elapsed Time, 185598 HSPs Collected
Number of families returned by RECON: 3449
Round Time: 00:15:45 (hh:mm:ss) Elapsed Time : 8 families discovered.

RepeatScout/RECON discovery complete: 26 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.qgnAGq/RM_4170205.TueSep90454062025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:20:59 (hh:mm:ss) Elapsed Time