RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.cCvds2/RM_3679455.TueSep91810462025
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: 1757466645
Database = /dev/shm/rModeler.cCvds2/GCA_011762635.1_ASM1176263v1 
  - Sequences = 4780
  - Bases = 25774670
  - N50 = 36386
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  157719-168971 |                                                   [ 1 ]
  146468-157719 |                                                   [  ]
  135216-146467 |                                                   [ 3 ]
  123965-135216 |                                                   [  ]
  112714-123965 |                                                   [ 4 ]
  101462-112713 |                                                   [ 5 ]
  90211-101462  |                                                   [ 11 ]
  78959-90210   |                                                   [ 21 ]
  67708-78959   |                                                   [ 23 ]
  56457-67708   |                                                   [ 25 ]
  45205-56456   |                                                   [ 55 ]
  33954-45205   |                                                   [ 78 ]
  22702-33953   |*                                                  [ 156 ]
  11451-22702   |**                                                 [ 226 ]
  200-11451     |************************************************** [ 4172 ]

Storage Throughput = excellent ( 1086.90 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 25774584 bp ( 25771850 non ambiguous )
   - Num Contigs Represented = 4780
   - 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.. : 279 raw families identified
   - RepeatScout: Running filtering stage.. 275 families remaining
   - RepeatScout: 00:02:08 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 265 families... 00:00:42 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 69 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:03:00 (hh:mm:ss) Elapsed Time : 196 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 00:00:17 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4102 repeats masked totaling 1045693 bp(s).
   - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10023368 bp
       Num Contigs Represented = 1878
       Non ambiguous bp:
             Initial: 10022648 bp
             After Masking: 8948852 bp
             Masked: 10.71 % 
 -- Input Database Coverage: 10023368 bp out of 25774670 bp ( 38.89 % )
Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1826916
Comparison Time: 00:13:55 (hh:mm:ss) Elapsed Time, 7754 HSPs Collected
Number of families returned by RECON: 1888
Round Time: 00:14:55 (hh:mm:ss) Elapsed Time : 11 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 00:00:25 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6917 repeats masked totaling 1696856 bp(s).
   - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 15751139 bp
       Num Contigs Represented = 2992
       Non ambiguous bp:
             Initial: 15749125 bp
             After Masking: 14004172 bp
             Masked: 11.08 % 
 -- Input Database Coverage: 25774507 bp out of 25774670 bp ( 100.00 % )
Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 4797253
Comparison Time: 00:25:48 (hh:mm:ss) Elapsed Time, 14655 HSPs Collected
Number of families returned by RECON: 3451
Round Time: 00:27:15 (hh:mm:ss) Elapsed Time : 21 families discovered.

RepeatScout/RECON discovery complete: 228 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.cCvds2/RM_3679455.TueSep91810462025
# 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: 00:46:11 (hh:mm:ss) Elapsed Time