RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.ftYBoG/RM_2623206.TueFeb101043082026
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: 1770748988
Database = /dev/shm/rModeler.ftYBoG/GCA_900617875.1_Pyy33X-2 
  - Sequences = 2303
  - Bases = 22457976
  - N50 = 1769872
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2458973-2634606 |                                                   [ 2 ]
  2283341-2458973 |                                                   [  ]
  2107708-2283340 |                                                   [  ]
  1932076-2107708 |                                                   [  ]
  1756444-1932076 |                                                   [ 3 ]
  1580811-1756443 |                                                   [ 1 ]
  1405179-1580811 |                                                   [ 1 ]
  1229546-1405178 |                                                   [  ]
  1053914-1229546 |                                                   [ 1 ]
  878282-1053914  |                                                   [ 1 ]
  702649-878281   |                                                   [ 3 ]
  527017-702649   |                                                   [ 2 ]
  351384-527016   |                                                   [  ]
  175752-351384   |                                                   [  ]
  120-175752      |************************************************** [ 2289 ]

Storage Throughput = excellent ( 1537.72 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 22457855 bp ( 22408426 non ambiguous )
   - Num Contigs Represented = 2302
   - 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.. : 155 raw families identified
   - RepeatScout: Running filtering stage.. 75 families remaining
   - RepeatScout: 00:01:42 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 68 families... 00:00:58 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 21 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 : 47 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 00:00:54 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2927 repeats masked totaling 1910219 bp(s).
   - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10042976 bp
       Num Contigs Represented = 1037
       Non ambiguous bp:
             Initial: 10021390 bp
             After Masking: 7736691 bp
             Masked: 22.80 % 
 -- Input Database Coverage: 10042976 bp out of 22457976 bp ( 44.72 % )
Sampling Time: 00:01:36 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 783126
Comparison Time: 00:24:46 (hh:mm:ss) Elapsed Time, 3391 HSPs Collected
Number of families returned by RECON: 276
Round Time: 00:26:41 (hh:mm:ss) Elapsed Time : 5 families discovered.
   - Increasing sample size to include end piece now = 42457976


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 42457976 bp
   - Sequence extraction : 00:00:01 (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...
       3816 repeats masked totaling 2358068 bp(s).
   - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 12414799 bp
       Num Contigs Represented = 1282
       Non ambiguous bp:
             Initial: 12386956 bp
             After Masking: 9543395 bp
             Masked: 22.96 % 
 -- Input Database Coverage: 22457775 bp out of 22457976 bp ( 100.00 % )
Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1202025
Comparison Time: 00:35:39 (hh:mm:ss) Elapsed Time, 1292 HSPs Collected
Number of families returned by RECON: 316
Round Time: 00:37:55 (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.ftYBoG/RM_2623206.TueFeb101043082026
# 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: 01:07:37 (hh:mm:ss) Elapsed Time