RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.Zp570p/RM_3151567.TueFeb101147552026
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: 1770752875
Database = /dev/shm/rModeler.Zp570p/GCA_900617845.1_Pyy1.1-2 
  - Sequences = 2308
  - Bases = 22276532
  - N50 = 1727870
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2510001-2689276 |                                                   [ 2 ]
  2330727-2510001 |                                                   [  ]
  2151453-2330727 |                                                   [  ]
  1972178-2151452 |                                                   [  ]
  1792904-1972178 |                                                   [  ]
  1613630-1792904 |                                                   [ 4 ]
  1434355-1613629 |                                                   [ 1 ]
  1255081-1434355 |                                                   [  ]
  1075807-1255081 |                                                   [  ]
  896532-1075806  |                                                   [ 2 ]
  717258-896532   |                                                   [ 2 ]
  537984-717258   |                                                   [ 3 ]
  358709-537983   |                                                   [  ]
  179435-358709   |                                                   [  ]
  161-179435      |************************************************** [ 2294 ]

Storage Throughput = excellent ( 1748.47 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 22276507 bp ( 22212336 non ambiguous )
   - Num Contigs Represented = 2308
   - 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.. : 150 raw families identified
   - RepeatScout: Running filtering stage.. 78 families remaining
   - RepeatScout: 00:01:46 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 75 families... 00:00:43 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 27 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:02:33 (hh:mm:ss) Elapsed Time : 48 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 00:00:55 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2550 repeats masked totaling 1776128 bp(s).
   - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10049547 bp
       Num Contigs Represented = 1009
       Non ambiguous bp:
             Initial: 10015944 bp
             After Masking: 7899218 bp
             Masked: 21.13 % 
 -- Input Database Coverage: 10049547 bp out of 22276532 bp ( 45.11 % )
Sampling Time: 00:01:40 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 741153
Comparison Time: 00:24:42 (hh:mm:ss) Elapsed Time, 1362 HSPs Collected
Number of families returned by RECON: 258
Round Time: 00:26:28 (hh:mm:ss) Elapsed Time : 4 families discovered.
   - Increasing sample size to include end piece now = 42276532


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 42276532 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3902 repeats masked totaling 2479197 bp(s).
   - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 12226913 bp
       Num Contigs Represented = 1319
       Non ambiguous bp:
             Initial: 12196345 bp
             After Masking: 9281683 bp
             Masked: 23.90 % 
 -- Input Database Coverage: 22276460 bp out of 22276532 bp ( 100.00 % )
Sampling Time: 00:02:03 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1242676
Comparison Time: 00:33:21 (hh:mm:ss) Elapsed Time, 965 HSPs Collected
Number of families returned by RECON: 265
Round Time: 00:35:29 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 53 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.Zp570p/RM_3151567.TueFeb101147552026
# 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: 00:00:17 (hh:mm:ss) Elapsed Time


Program Time: 01:04:47 (hh:mm:ss) Elapsed Time