RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.itF8rs/RM_3158172.WedSep101419302025
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: 1757539169
Database = /dev/shm/rModeler.itF8rs/GCA_018154715.1_ASM1815471v1 
  - Sequences = 330
  - Bases = 19500729
  - N50 = 420881
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1469099-1574021 |                                                   [ 1 ]
  1364178-1469099 |                                                   [  ]
  1259256-1364177 |                                                   [  ]
  1154335-1259256 |                                                   [  ]
  1049414-1154335 |                                                   [ 1 ]
  944492-1049413  |                                                   [ 1 ]
  839571-944492   |                                                   [  ]
  734649-839570   |                                                   [ 1 ]
  629728-734649   |                                                   [ 2 ]
  524807-629728   |                                                   [ 4 ]
  419885-524806   |                                                   [ 3 ]
  314964-419885   |*                                                  [ 6 ]
  210042-314963   |**                                                 [ 13 ]
  105121-210042   |***                                                [ 17 ]
  200-105121      |************************************************** [ 281 ]

Storage Throughput = excellent ( 1512.07 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19500711 bp ( 19493867 non ambiguous )
   - Num Contigs Represented = 330
   - Sequence extraction : 00:00:00 (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: 00:00:27 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 5 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:33 (hh:mm:ss) Elapsed Time : 13 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...
       282 repeats masked totaling 52713 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10010585 bp
       Num Contigs Represented = 176
       Non ambiguous bp:
             Initial: 10006565 bp
             After Masking: 9897019 bp
             Masked: 1.09 % 
 -- Input Database Coverage: 10010585 bp out of 19500729 bp ( 51.33 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 70500
Comparison Time: 00:04:41 (hh:mm:ss) Elapsed Time, 20033 HSPs Collected
Number of families returned by RECON: 1606
Round Time: 00:05:16 (hh:mm:ss) Elapsed Time : 4 families discovered.
   - Increasing sample size to include end piece now = 39500729


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39500729 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...
       1771 repeats masked totaling 174507 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9490066 bp
       Num Contigs Represented = 210
       Non ambiguous bp:
             Initial: 9487242 bp
             After Masking: 9263984 bp
             Masked: 2.35 % 
 -- Input Database Coverage: 19500651 bp out of 19500729 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 77421
Comparison Time: 00:04:12 (hh:mm:ss) Elapsed Time, 2919 HSPs Collected
Number of families returned by RECON: 849
Round Time: 00:04:29 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 18 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.itF8rs/RM_3158172.WedSep101419302025
# 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: 00:00:05 (hh:mm:ss) Elapsed Time


Program Time: 00:10:23 (hh:mm:ss) Elapsed Time