RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.w1fiAV/RM_2620756.TueFeb101042522026
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: 1770748972
Database = /dev/shm/rModeler.w1fiAV/GCA_900617885.1_Pyy3AE-2 
  - Sequences = 3182
  - Bases = 22809207
  - N50 = 1723897
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2526077-2706502 |                                                   [ 2 ]
  2345652-2526076 |                                                   [  ]
  2165227-2345651 |                                                   [  ]
  1984802-2165226 |                                                   [  ]
  1804378-1984802 |                                                   [  ]
  1623953-1804377 |                                                   [ 4 ]
  1443528-1623952 |                                                   [ 1 ]
  1263103-1443527 |                                                   [  ]
  1082678-1263102 |                                                   [  ]
  902254-1082678  |                                                   [ 2 ]
  721829-902253   |                                                   [ 3 ]
  541404-721828   |                                                   [ 1 ]
  360979-541403   |                                                   [ 1 ]
  180554-360978   |                                                   [  ]
  130-180554      |************************************************** [ 3168 ]

Storage Throughput = excellent ( 1616.78 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 22809011 bp ( 22727470 non ambiguous )
   - Num Contigs Represented = 3181
   - 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.. : 164 raw families identified
   - RepeatScout: Running filtering stage.. 80 families remaining
   - RepeatScout: 00:01:46 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 77 families... 00:05:09 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 24 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:07:00 (hh:mm:ss) Elapsed Time : 53 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3001 repeats masked totaling 2025736 bp(s).
   - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10051430 bp
       Num Contigs Represented = 1421
       Non ambiguous bp:
             Initial: 10011467 bp
             After Masking: 7643679 bp
             Masked: 23.65 % 
 -- Input Database Coverage: 10051430 bp out of 22809207 bp ( 44.07 % )
Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1319500
Comparison Time: 00:25:16 (hh:mm:ss) Elapsed Time, 2372 HSPs Collected
Number of families returned by RECON: 265
Round Time: 00:27:23 (hh:mm:ss) Elapsed Time : 4 families discovered.
   - Increasing sample size to include end piece now = 42809207


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 42809207 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...
       3936 repeats masked totaling 2672649 bp(s).
   - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 12757501 bp
       Num Contigs Represented = 1783
       Non ambiguous bp:
             Initial: 12715923 bp
             After Masking: 9613524 bp
             Masked: 24.40 % 
 -- Input Database Coverage: 22808931 bp out of 22809207 bp ( 100.00 % )
Sampling Time: 00:02:04 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2089990
Comparison Time: 00:34:42 (hh:mm:ss) Elapsed Time, 1320 HSPs Collected
Number of families returned by RECON: 349
Round Time: 00:36:51 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 58 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.w1fiAV/RM_2620756.TueFeb101042522026
# 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: 00:00:16 (hh:mm:ss) Elapsed Time


Program Time: 01:11:30 (hh:mm:ss) Elapsed Time