RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.76xU4E/RM_1739964.FriSep122050132025
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: 1757735412
Database = /dev/shm/rModeler.76xU4E/GCA_051527475.1_YNP33 
  - Sequences = 1719
  - Bases = 30433171
  - N50 = 36540
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  150888-161595 |                                                   [ 3 ]
  140182-150888 |                                                   [ 1 ]
  129476-140182 |                                                   [ 2 ]
  118770-129476 |                                                   [ 3 ]
  108064-118770 |                                                   [ 5 ]
  97357-108063  |                                                   [ 8 ]
  86651-97357   |                                                   [ 11 ]
  75945-86651   |                                                   [ 19 ]
  65239-75945   |*                                                  [ 29 ]
  54533-65239   |*                                                  [ 38 ]
  43826-54532   |***                                                [ 61 ]
  33120-43826   |*****                                              [ 114 ]
  22414-33120   |********                                           [ 163 ]
  11708-22414   |****************                                   [ 306 ]
  1002-11708    |************************************************** [ 956 ]

Storage Throughput = excellent ( 1749.49 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 30433101 bp ( 30423975 non ambiguous )
   - Num Contigs Represented = 1719
   - 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.. : 185 raw families identified
   - RepeatScout: Running filtering stage.. 184 families remaining
   - RepeatScout: 00:00:49 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 177 families... 00:00:24 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 52 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:16 (hh:mm:ss) Elapsed Time : 125 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2585 repeats masked totaling 594656 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10015443 bp
       Num Contigs Represented = 626
       Non ambiguous bp:
             Initial: 10011725 bp
             After Masking: 9378697 bp
             Masked: 6.32 % 
 -- Input Database Coverage: 10015443 bp out of 30433171 bp ( 32.91 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 221445
Comparison Time: 00:05:14 (hh:mm:ss) Elapsed Time, 9652 HSPs Collected
Number of families returned by RECON: 1505
Round Time: 00:05:41 (hh:mm:ss) Elapsed Time : 17 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (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...
       7619 repeats masked totaling 1502605 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 20417583 bp
       Num Contigs Represented = 1210
       Non ambiguous bp:
             Initial: 20412175 bp
             After Masking: 18826591 bp
             Masked: 7.77 % 
 -- Input Database Coverage: 30433026 bp out of 30433171 bp ( 100.00 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 886446
Comparison Time: 00:12:03 (hh:mm:ss) Elapsed Time, 28092 HSPs Collected
Number of families returned by RECON: 3138
Round Time: 00:13:00 (hh:mm:ss) Elapsed Time : 65 families discovered.

RepeatScout/RECON discovery complete: 207 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.76xU4E/RM_1739964.FriSep122050132025
# 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: 00:20:15 (hh:mm:ss) Elapsed Time