RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.wOte2S/RM_1217518.TueFeb101048362026
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: 1770749315
Database = /dev/shm/rModeler.wOte2S/GCA_900617865.1_Pyy2CL-2 
  - Sequences = 2915
  - Bases = 22722262
  - N50 = 1732069
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2518681-2698579 |                                                   [ 2 ]
  2338784-2518681 |                                                   [  ]
  2158887-2338784 |                                                   [  ]
  1978990-2158887 |                                                   [  ]
  1799093-1978990 |                                                   [ 2 ]
  1619196-1799093 |                                                   [ 2 ]
  1439299-1619196 |                                                   [ 1 ]
  1259401-1439298 |                                                   [  ]
  1079504-1259401 |                                                   [  ]
  899607-1079504  |                                                   [ 2 ]
  719710-899607   |                                                   [ 2 ]
  539813-719710   |                                                   [ 2 ]
  359916-539813   |                                                   [ 1 ]
  180019-359916   |                                                   [  ]
  122-180019      |************************************************** [ 2901 ]

Storage Throughput = excellent ( 1586.02 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 22722109 bp ( 22663109 non ambiguous )
   - Num Contigs Represented = 2914
   - 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.. : 158 raw families identified
   - RepeatScout: Running filtering stage.. 78 families remaining
   - RepeatScout: 00:01:45 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 75 families... 00:00:53 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 17 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:02:44 (hh:mm:ss) Elapsed Time : 58 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...
       3232 repeats masked totaling 1895486 bp(s).
   - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10038320 bp
       Num Contigs Represented = 1292
       Non ambiguous bp:
             Initial: 10014344 bp
             After Masking: 7761846 bp
             Masked: 22.49 % 
 -- Input Database Coverage: 10038320 bp out of 22722262 bp ( 44.18 % )
Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1127251
Comparison Time: 00:25:33 (hh:mm:ss) Elapsed Time, 3005 HSPs Collected
Number of families returned by RECON: 269
Round Time: 00:27:29 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 42722262


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 42722262 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4524 repeats masked totaling 2695481 bp(s).
   - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 12683756 bp
       Num Contigs Represented = 1638
       Non ambiguous bp:
             Initial: 12648732 bp
             After Masking: 9525342 bp
             Masked: 24.69 % 
 -- Input Database Coverage: 22722076 bp out of 22722262 bp ( 100.00 % )
Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1807851
Comparison Time: 00:34:59 (hh:mm:ss) Elapsed Time, 1594 HSPs Collected
Number of families returned by RECON: 334
Round Time: 00:37:14 (hh:mm:ss) Elapsed Time : 4 families discovered.

RepeatScout/RECON discovery complete: 65 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.wOte2S/RM_1217518.TueFeb101048362026
# 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: 00:00:18 (hh:mm:ss) Elapsed Time


Program Time: 01:07:45 (hh:mm:ss) Elapsed Time