RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.azJCML/RM_64058.ThuFeb120605082026
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: 1770905107
Database = /dev/shm/rModeler.azJCML/GCA_030569475.1_ASM3056947v1 
  - Sequences = 110
  - Bases = 13312851
  - N50 = 323378
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1522048-1630725 |                                                   [ 1 ]
  1413372-1522048 |                                                   [  ]
  1304695-1413371 |                                                   [  ]
  1196019-1304695 |                                                   [  ]
  1087342-1196018 |                                                   [  ]
  978666-1087342  |                                                   [ 1 ]
  869989-978665   |                                                   [  ]
  761313-869989   |                                                   [  ]
  652636-761312   |                                                   [ 1 ]
  543960-652636   |                                                   [ 1 ]
  435283-543959   |                                                   [  ]
  326607-435283   |***                                                [ 5 ]
  217930-326606   |*******                                            [ 10 ]
  109254-217930   |**************                                     [ 20 ]
  578-109254      |************************************************** [ 71 ]

Storage Throughput = excellent ( 1654.36 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 13312753 bp ( 13306953 non ambiguous )
   - Num Contigs Represented = 110
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 18 raw families identified
   - RepeatScout: Running filtering stage.. 17 families remaining
   - RepeatScout: 00:00:17 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 13 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 3 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:23 (hh:mm:ss) Elapsed Time : 10 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 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       142 repeats masked totaling 41088 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10011533 bp
       Num Contigs Represented = 95
       Non ambiguous bp:
             Initial: 10007133 bp
             After Masking: 9925697 bp
             Masked: 0.81 % 
 -- Input Database Coverage: 10011533 bp out of 13312851 bp ( 75.20 % )
Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 47586
Comparison Time: 00:03:44 (hh:mm:ss) Elapsed Time, 4275 HSPs Collected
Number of families returned by RECON: 878
Round Time: 00:03:57 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 33312851


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 33312851 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       50 repeats masked totaling 12957 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 3301181 bp
       Num Contigs Represented = 53
       Non ambiguous bp:
             Initial: 3299781 bp
             After Masking: 3279380 bp
             Masked: 0.62 % 
 -- Input Database Coverage: 13312714 bp out of 13312851 bp ( 100.00 % )
Sampling Time: 00:00:04 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 5356
Comparison Time: 00:01:01 (hh:mm:ss) Elapsed Time, 246 HSPs Collected
Number of families returned by RECON: 149
Round Time: 00:01:06 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 11 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.azJCML/RM_64058.ThuFeb120605082026
# 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: 00:05:31 (hh:mm:ss) Elapsed Time