RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.eh0d1i/RM_1764819.ThuSep110153592025
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: 1757580838
Database = /dev/shm/rModeler.eh0d1i/GCA_022288605.1_ASM2228860v1 
  - Sequences = 1528
  - Bases = 30077648
  - N50 = 38386
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  192901-206609 |                                                   [ 1 ]
  179194-192901 |                                                   [ 1 ]
  165487-179194 |                                                   [ 1 ]
  151780-165487 |                                                   [ 2 ]
  138073-151780 |                                                   [ 2 ]
  124365-138072 |                                                   [ 4 ]
  110658-124365 |                                                   [ 5 ]
  96951-110658  |                                                   [ 9 ]
  83244-96951   |                                                   [ 11 ]
  69537-83244   |*                                                  [ 27 ]
  55829-69536   |**                                                 [ 45 ]
  42122-55829   |*****                                              [ 103 ]
  28415-42122   |*******                                            [ 135 ]
  14708-28415   |*****************                                  [ 302 ]
  1001-14708    |*************************************************  [ 880 ]

Storage Throughput = excellent ( 1551.92 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 30077604 bp ( 30071085 non ambiguous )
   - Num Contigs Represented = 1528
   - 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.. : 120 raw families identified
   - RepeatScout: Running filtering stage.. 119 families remaining
   - RepeatScout: 00:00:48 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 112 families... 00:00:16 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 31 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:08 (hh:mm:ss) Elapsed Time : 81 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1709 repeats masked totaling 535465 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10022652 bp
       Num Contigs Represented = 581
       Non ambiguous bp:
             Initial: 10020693 bp
             After Masking: 9448691 bp
             Masked: 5.71 % 
 -- Input Database Coverage: 10022652 bp out of 30077648 bp ( 33.32 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 189420
Comparison Time: 00:05:18 (hh:mm:ss) Elapsed Time, 15171 HSPs Collected
Number of families returned by RECON: 1666
Round Time: 00:05:45 (hh:mm:ss) Elapsed Time : 30 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6654 repeats masked totaling 1261181 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 20054915 bp
       Num Contigs Represented = 1063
       Non ambiguous bp:
             Initial: 20050355 bp
             After Masking: 18721693 bp
             Masked: 6.63 % 
 -- Input Database Coverage: 30077567 bp out of 30077648 bp ( 100.00 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 713415
Comparison Time: 00:11:47 (hh:mm:ss) Elapsed Time, 25017 HSPs Collected
Number of families returned by RECON: 3060
Round Time: 00:12:29 (hh:mm:ss) Elapsed Time : 57 families discovered.

RepeatScout/RECON discovery complete: 168 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.eh0d1i/RM_1764819.ThuSep110153592025
# 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: 00:00:17 (hh:mm:ss) Elapsed Time


Program Time: 00:19:39 (hh:mm:ss) Elapsed Time