RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.5dUKpm/RM_3625423.FriSep120315512025
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: 1757672151
Database = /data/tmp/rModeler.5dUKpm/GCA_032356565.1_MYCT-2043-2021 
  - Sequences = 325
  - Bases = 14810204
  - N50 = 110847
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  409692-438920 |                                                   [ 1 ]
  380464-409691 |                                                   [  ]
  351237-380464 |                                                   [  ]
  322009-351236 |                                                   [  ]
  292781-322008 |                                                   [ 1 ]
  263554-292781 |                                                   [ 1 ]
  234326-263553 |                                                   [ 1 ]
  205098-234325 |*                                                  [ 5 ]
  175871-205098 |*                                                  [ 4 ]
  146643-175870 |**                                                 [ 8 ]
  117415-146642 |****                                               [ 15 ]
  88188-117415  |******                                             [ 25 ]
  58960-88187   |*********                                          [ 33 ]
  29732-58959   |*************                                      [ 48 ]
  505-29732     |************************************************** [ 183 ]

Storage Throughput = good ( 741.77 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14810099 bp ( 14659242 non ambiguous )
   - Num Contigs Represented = 325
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 41 raw families identified
   - RepeatScout: Running filtering stage.. 37 families remaining
   - RepeatScout: 00:02:21 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 32 families... 00:00:28 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 1 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:02:55 (hh:mm:ss) Elapsed Time : 31 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 00:00:31 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       589 repeats masked totaling 245974 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10115904 bp
       Num Contigs Represented = 250
       Non ambiguous bp:
             Initial: 10002325 bp
             After Masking: 9643435 bp
             Masked: 3.59 % 
 -- Input Database Coverage: 10115904 bp out of 14810204 bp ( 68.30 % )
Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 75078
Comparison Time: 00:11:19 (hh:mm:ss) Elapsed Time, 3335 HSPs Collected
Number of families returned by RECON: 981
Round Time: 00:12:39 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 34810204


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34810204 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       282 repeats masked totaling 111130 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4694183 bp
       Num Contigs Represented = 155
       Non ambiguous bp:
             Initial: 4656905 bp
             After Masking: 4495728 bp
             Masked: 3.46 % 
 -- Input Database Coverage: 14810087 bp out of 14810204 bp ( 100.00 % )
Sampling Time: 00:00:20 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 18336
Comparison Time: 00:04:08 (hh:mm:ss) Elapsed Time, 712 HSPs Collected
Number of families returned by RECON: 306
Round Time: 00:04:39 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 33 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.5dUKpm/RM_3625423.FriSep120315512025
# 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: 00:00:21 (hh:mm:ss) Elapsed Time


Program Time: 00:20:34 (hh:mm:ss) Elapsed Time