RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.ZvygCr/RM_2970822.MonSep81722482025
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: 1757377367
Database = /data/tmp/rModeler.ZvygCr/GCA_002215775.1_Cryp_neof_AD2_60a_V1 
  - Sequences = 168
  - Bases = 18629733
  - N50 = 749990
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1456261-1560208 |                                                   [ 1 ]
  1352314-1456260 |                                                   [  ]
  1248367-1352313 |                                                   [  ]
  1144420-1248366 |                                                   [ 1 ]
  1040473-1144419 |                                                   [ 1 ]
  936526-1040472  |                                                   [  ]
  832579-936525   |                                                   [ 2 ]
  728632-832578   |*                                                  [ 5 ]
  624685-728631   |                                                   [ 1 ]
  520738-624684   |*                                                  [ 5 ]
  416791-520737   |*                                                  [ 4 ]
  312844-416790   |*                                                  [ 4 ]
  208897-312843   |                                                   [ 2 ]
  104950-208896   |*                                                  [ 5 ]
  1004-104950     |*************************************************  [ 137 ]

Storage Throughput = good ( 831.18 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18629676 bp ( 18548323 non ambiguous )
   - Num Contigs Represented = 168
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 44 raw families identified
   - RepeatScout: Running filtering stage.. 44 families remaining
   - RepeatScout: 00:00:35 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 43 families... 00:00:17 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:59 (hh:mm:ss) Elapsed Time : 41 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       697 repeats masked totaling 335442 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10047686 bp
       Num Contigs Represented = 109
       Non ambiguous bp:
             Initial: 10008030 bp
             After Masking: 9663221 bp
             Masked: 3.45 % 
 -- Input Database Coverage: 10047686 bp out of 18629733 bp ( 53.93 % )
Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 52975
Comparison Time: 00:06:47 (hh:mm:ss) Elapsed Time, 2325 HSPs Collected
Number of families returned by RECON: 709
Round Time: 00:07:36 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 38629733


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38629733 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       663 repeats masked totaling 319084 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8581910 bp
       Num Contigs Represented = 94
       Non ambiguous bp:
             Initial: 8540213 bp
             After Masking: 8212985 bp
             Masked: 3.83 % 
 -- Input Database Coverage: 18629596 bp out of 18629733 bp ( 100.00 % )
Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 39340
Comparison Time: 00:05:38 (hh:mm:ss) Elapsed Time, 1199 HSPs Collected
Number of families returned by RECON: 482
Round Time: 00:06:06 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 43 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.ZvygCr/RM_2970822.MonSep81722482025
# 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: 00:00:31 (hh:mm:ss) Elapsed Time


Program Time: 00:15:12 (hh:mm:ss) Elapsed Time