RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.nu7FyB/RM_3429844.TueFeb101150502026
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: 1770753050
Database = /dev/shm/rModeler.nu7FyB/GCA_900617855.1_Pyy1AR-2 
  - Sequences = 2475
  - Bases = 22459875
  - N50 = 1795283
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2413186-2585550 |                                                   [ 2 ]
  2240823-2413186 |                                                   [  ]
  2068460-2240823 |                                                   [  ]
  1896097-2068460 |                                                   [  ]
  1723734-1896097 |                                                   [ 4 ]
  1551370-1723733 |                                                   [  ]
  1379007-1551370 |                                                   [ 1 ]
  1206644-1379007 |                                                   [  ]
  1034281-1206644 |                                                   [  ]
  861918-1034281  |                                                   [ 2 ]
  689554-861917   |                                                   [ 3 ]
  517191-689554   |                                                   [ 2 ]
  344828-517191   |                                                   [  ]
  172465-344828   |                                                   [  ]
  102-172465      |************************************************** [ 2461 ]

Storage Throughput = excellent ( 1674.83 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 22459753 bp ( 22371348 non ambiguous )
   - Num Contigs Represented = 2474
   - 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.. : 140 raw families identified
   - RepeatScout: Running filtering stage.. 74 families remaining
   - RepeatScout: 00:01:44 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 70 families... 00:01:10 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 25 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:02:58 (hh:mm:ss) Elapsed Time : 45 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...
       2850 repeats masked totaling 2067482 bp(s).
   - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10031356 bp
       Num Contigs Represented = 1161
       Non ambiguous bp:
             Initial: 10005240 bp
             After Masking: 7601955 bp
             Masked: 24.02 % 
 -- Input Database Coverage: 10031356 bp out of 22459875 bp ( 44.66 % )
Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 939135
Comparison Time: 00:24:00 (hh:mm:ss) Elapsed Time, 2570 HSPs Collected
Number of families returned by RECON: 251
Round Time: 00:26:03 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 42459875


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 42459875 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3093 repeats masked totaling 2193951 bp(s).
   - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 12428341 bp
       Num Contigs Represented = 1333
       Non ambiguous bp:
             Initial: 12366052 bp
             After Masking: 9728888 bp
             Masked: 21.33 % 
 -- Input Database Coverage: 22459697 bp out of 22459875 bp ( 100.00 % )
Sampling Time: 00:01:52 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1260078
Comparison Time: 00:36:22 (hh:mm:ss) Elapsed Time, 1494 HSPs Collected
Number of families returned by RECON: 386
Round Time: 00:38:18 (hh:mm:ss) Elapsed Time : 3 families discovered.

RepeatScout/RECON discovery complete: 51 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.nu7FyB/RM_3429844.TueFeb101150502026
# 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: 00:00:15 (hh:mm:ss) Elapsed Time


Program Time: 01:07:34 (hh:mm:ss) Elapsed Time