RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.0iSIz3/RM_2987385.ThuSep110025272025
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: 1757575526
Database = /dev/shm/rModeler.0iSIz3/GCA_021018935.2_ASM2101893v2 
  - Sequences = 1822
  - Bases = 14443128
  - N50 = 30478
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  164267-175987 |                                                   [ 1 ]
  152548-164267 |                                                   [ 1 ]
  140829-152548 |                                                   [  ]
  129110-140829 |                                                   [ 1 ]
  117391-129110 |                                                   [ 2 ]
  105672-117391 |                                                   [ 2 ]
  93953-105672  |                                                   [  ]
  82233-93952   |                                                   [ 10 ]
  70514-82233   |                                                   [ 5 ]
  58795-70514   |                                                   [ 16 ]
  47076-58795   |                                                   [ 24 ]
  35357-47076   |*                                                  [ 44 ]
  23638-35357   |**                                                 [ 83 ]
  11919-23638   |*****                                              [ 170 ]
  200-11919     |************************************************** [ 1463 ]

Storage Throughput = excellent ( 1102.06 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 14443019 bp ( 14057104 non ambiguous )
   - Num Contigs Represented = 1822
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 13, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 39 raw families identified
   - RepeatScout: Running filtering stage.. 37 families remaining
   - RepeatScout: 00:02:44 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 35 families... 00:00:11 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:03:02 (hh:mm:ss) Elapsed Time : 31 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 00:00:22 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       544 repeats masked totaling 154229 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10288579 bp
       Num Contigs Represented = 1330
       Non ambiguous bp:
             Initial: 10011903 bp
             After Masking: 9823422 bp
             Masked: 1.88 % 
 -- Input Database Coverage: 10288579 bp out of 14443128 bp ( 71.24 % )
Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 957036
Comparison Time: 00:14:00 (hh:mm:ss) Elapsed Time, 5081 HSPs Collected
Number of families returned by RECON: 1306
Round Time: 00:14:47 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 34443128


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 34443128 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       310 repeats masked totaling 70518 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 4154398 bp
       Num Contigs Represented = 532
       Non ambiguous bp:
             Initial: 4045159 bp
             After Masking: 3961861 bp
             Masked: 2.06 % 
 -- Input Database Coverage: 14442977 bp out of 14443128 bp ( 100.00 % )
Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 148785
Comparison Time: 00:04:05 (hh:mm:ss) Elapsed Time, 932 HSPs Collected
Number of families returned by RECON: 325
Round Time: 00:04:19 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 33 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.0iSIz3/RM_2987385.ThuSep110025272025
# 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: 00:22:23 (hh:mm:ss) Elapsed Time