RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.fZIBvG/RM_3069471.WedSep101412512025
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: 1757538771
Database = /dev/shm/rModeler.fZIBvG/GCA_018154565.1_ASM1815456v1 
  - Sequences = 316
  - Bases = 19554160
  - N50 = 558822
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1742862-1867338 |                                                   [ 1 ]
  1618386-1742861 |                                                   [  ]
  1493910-1618385 |                                                   [ 1 ]
  1369434-1493909 |                                                   [  ]
  1244958-1369433 |                                                   [  ]
  1120482-1244957 |                                                   [  ]
  996006-1120481  |                                                   [  ]
  871531-996006   |                                                   [ 1 ]
  747055-871530   |                                                   [ 2 ]
  622579-747054   |                                                   [ 3 ]
  498103-622578   |*                                                  [ 6 ]
  373627-498102   |                                                   [ 4 ]
  249151-373626   |*                                                  [ 10 ]
  124675-249150   |**                                                 [ 12 ]
  200-124675      |************************************************** [ 276 ]

Storage Throughput = excellent ( 1446.65 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19554092 bp ( 19551320 non ambiguous )
   - Num Contigs Represented = 316
   - 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.. : 26 raw families identified
   - RepeatScout: Running filtering stage.. 26 families remaining
   - RepeatScout: 00:00:27 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 25 families... 00:00:07 (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: 00:00:37 (hh:mm:ss) Elapsed Time : 21 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       379 repeats masked totaling 64451 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10015092 bp
       Num Contigs Represented = 179
       Non ambiguous bp:
             Initial: 10013367 bp
             After Masking: 9894282 bp
             Masked: 1.19 % 
 -- Input Database Coverage: 10015092 bp out of 19554160 bp ( 51.22 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 73920
Comparison Time: 00:04:45 (hh:mm:ss) Elapsed Time, 16253 HSPs Collected
Number of families returned by RECON: 1507
Round Time: 00:05:09 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 39554160


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39554160 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...
       376 repeats masked totaling 60617 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9538931 bp
       Num Contigs Represented = 181
       Non ambiguous bp:
             Initial: 9537884 bp
             After Masking: 9423910 bp
             Masked: 1.19 % 
 -- Input Database Coverage: 19554023 bp out of 19554160 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 71631
Comparison Time: 00:04:29 (hh:mm:ss) Elapsed Time, 16762 HSPs Collected
Number of families returned by RECON: 1460
Round Time: 00:05:00 (hh:mm:ss) Elapsed Time : 5 families discovered.

RepeatScout/RECON discovery complete: 26 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.fZIBvG/RM_3069471.WedSep101412512025
# 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: 00:10:51 (hh:mm:ss) Elapsed Time