RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.ew36YW/RM_4063566.FriSep120158482025
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: 1757667527
Database = /dev/shm/rModeler.ew36YW/GCA_030582595.1_ASM3058259v1 
  - Sequences = 593
  - Bases = 14427693
  - N50 = 92909
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  289428-310066 |                                                   [ 2 ]
  268791-289428 |                                                   [ 1 ]
  248154-268791 |                                                   [  ]
  227516-248153 |                                                   [ 1 ]
  206879-227516 |                                                   [ 1 ]
  186242-206879 |                                                   [ 2 ]
  165604-186241 |                                                   [ 4 ]
  144967-165604 |                                                   [ 6 ]
  124330-144967 |                                                   [ 8 ]
  103692-124329 |*                                                  [ 14 ]
  83055-103692  |**                                                 [ 19 ]
  62418-83055   |**                                                 [ 24 ]
  41780-62417   |***                                                [ 32 ]
  21143-41780   |******                                             [ 54 ]
  506-21143     |************************************************** [ 425 ]

Storage Throughput = excellent ( 1726.09 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14427556 bp ( 14419056 non ambiguous )
   - Num Contigs Represented = 593
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 40 raw families identified
   - RepeatScout: Running filtering stage.. 39 families remaining
   - RepeatScout: 00:01:02 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 26 families... 00:00:11 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:17 (hh:mm:ss) Elapsed Time : 22 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       364 repeats masked totaling 136141 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10016078 bp
       Num Contigs Represented = 429
       Non ambiguous bp:
             Initial: 10010678 bp
             After Masking: 9801450 bp
             Masked: 2.09 % 
 -- Input Database Coverage: 10016078 bp out of 14427693 bp ( 69.42 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 156520
Comparison Time: 00:07:27 (hh:mm:ss) Elapsed Time, 4042 HSPs Collected
Number of families returned by RECON: 1082
Round Time: 00:07:51 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 34427693


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34427693 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       185 repeats masked totaling 64362 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4411403 bp
       Num Contigs Represented = 231
       Non ambiguous bp:
             Initial: 4408303 bp
             After Masking: 4309180 bp
             Masked: 2.25 % 
 -- Input Database Coverage: 14427481 bp out of 14427693 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33153
Comparison Time: 00:02:32 (hh:mm:ss) Elapsed Time, 930 HSPs Collected
Number of families returned by RECON: 311
Round Time: 00:02:50 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 23 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.ew36YW/RM_4063566.FriSep120158482025
# 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: 00:00:08 (hh:mm:ss) Elapsed Time


Program Time: 00:12:06 (hh:mm:ss) Elapsed Time