RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.AMBxF2/RM_1095830.ThuSep111446282025
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: 1757627187
Database = /dev/shm/rModeler.AMBxF2/GCA_025767685.1_ASM2576768v1 
  - Sequences = 1024
  - Bases = 15429135
  - N50 = 52172
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  284035-304288 |                                                   [ 2 ]
  263782-284034 |                                                   [ 1 ]
  243530-263782 |                                                   [ 1 ]
  223277-243529 |                                                   [ 1 ]
  203025-223277 |                                                   [  ]
  182772-203024 |                                                   [ 2 ]
  162520-182772 |                                                   [ 1 ]
  142267-162519 |                                                   [ 2 ]
  122015-142267 |                                                   [ 7 ]
  101762-122014 |                                                   [ 5 ]
  81510-101762  |                                                   [ 13 ]
  61257-81509   |*                                                  [ 18 ]
  41005-61257   |***                                                [ 52 ]
  20752-41004   |*******                                            [ 116 ]
  500-20752     |************************************************** [ 803 ]

Storage Throughput = excellent ( 1657.34 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 15429112 bp ( 14666969 non ambiguous )
   - Num Contigs Represented = 1024
   - 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.. : 28 raw families identified
   - RepeatScout: Running filtering stage.. 27 families remaining
   - RepeatScout: 00:01:04 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 27 families... 00:00:20 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:27 (hh:mm:ss) Elapsed Time : 27 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       407 repeats masked totaling 160727 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10526473 bp
       Num Contigs Represented = 731
       Non ambiguous bp:
             Initial: 10013669 bp
             After Masking: 9785495 bp
             Masked: 2.28 % 
 -- Input Database Coverage: 10526473 bp out of 15429135 bp ( 68.22 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 344035
Comparison Time: 00:07:45 (hh:mm:ss) Elapsed Time, 4144 HSPs Collected
Number of families returned by RECON: 1391
Round Time: 00:08:10 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 35429135


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 35429135 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...
       251 repeats masked totaling 65883 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4902591 bp
       Num Contigs Represented = 345
       Non ambiguous bp:
             Initial: 4653252 bp
             After Masking: 4555169 bp
             Masked: 2.11 % 
 -- Input Database Coverage: 15429064 bp out of 15429135 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 69006
Comparison Time: 00:03:01 (hh:mm:ss) Elapsed Time, 903 HSPs Collected
Number of families returned by RECON: 396
Round Time: 00:03:09 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.AMBxF2/RM_1095830.ThuSep111446282025
# 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: 00:00:07 (hh:mm:ss) Elapsed Time


Program Time: 00:12:53 (hh:mm:ss) Elapsed Time