RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.UhoOgC/RM_2619379.MonSep81635392025
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: 1757374539
Database = /data/tmp/rModeler.UhoOgC/GCA_002083735.1_Rhimi_ATCC11559_1 
  - Sequences = 595
  - Bases = 24077254
  - N50 = 85186
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  323883-346946 |                                                   [ 1 ]
  300820-323883 |                                                   [ 1 ]
  277757-300820 |                                                   [  ]
  254694-277757 |                                                   [ 1 ]
  231631-254694 |                                                   [ 1 ]
  208568-231631 |                                                   [ 5 ]
  185505-208568 |                                                   [ 5 ]
  162442-185505 |                                                   [ 4 ]
  139379-162442 |**                                                 [ 16 ]
  116316-139379 |**                                                 [ 18 ]
  93253-116316  |***                                                [ 19 ]
  70190-93253   |******                                             [ 39 ]
  47127-70190   |************                                       [ 74 ]
  24064-47127   |****************                                   [ 103 ]
  1001-24064    |************************************************** [ 308 ]

Storage Throughput = fair ( 661.65 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 24077175 bp ( 24037481 non ambiguous )
   - Num Contigs Represented = 595
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 157 raw families identified
   - RepeatScout: Running filtering stage.. 153 families remaining
   - RepeatScout: 00:01:35 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 148 families... 00:00:34 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 47 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:02:16 (hh:mm:ss) Elapsed Time : 101 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2417 repeats masked totaling 652808 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10030291 bp
       Num Contigs Represented = 328
       Non ambiguous bp:
             Initial: 10015846 bp
             After Masking: 9337831 bp
             Masked: 6.77 % 
 -- Input Database Coverage: 10030291 bp out of 24077254 bp ( 41.66 % )
Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 87153
Comparison Time: 00:09:20 (hh:mm:ss) Elapsed Time, 21669 HSPs Collected
Number of families returned by RECON: 1822
Round Time: 00:11:34 (hh:mm:ss) Elapsed Time : 14 families discovered.
   - Increasing sample size to include end piece now = 44077254


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 44077254 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4351 repeats masked totaling 1176745 bp(s).
   - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 14046804 bp
       Num Contigs Represented = 398
       Non ambiguous bp:
             Initial: 14021555 bp
             After Masking: 12802743 bp
             Masked: 8.69 % 
 -- Input Database Coverage: 24077095 bp out of 24077254 bp ( 100.00 % )
Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 161596
Comparison Time: 00:14:47 (hh:mm:ss) Elapsed Time, 10361 HSPs Collected
Number of families returned by RECON: 2664
Round Time: 00:16:59 (hh:mm:ss) Elapsed Time : 6 families discovered.

RepeatScout/RECON discovery complete: 121 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.UhoOgC/RM_2619379.MonSep81635392025
# 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: 00:00:41 (hh:mm:ss) Elapsed Time


Program Time: 00:31:30 (hh:mm:ss) Elapsed Time