RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.yetRhv/RM_1355960.TueSep90101482025
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: 1757404907
Database = /dev/shm/rModeler.yetRhv/GCA_003690965.1_ASM369096v1 
  - Sequences = 7904
  - Bases = 37946850
  - N50 = 125976
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  671853-719829 |                                                   [ 1 ]
  623878-671853 |                                                   [  ]
  575903-623878 |                                                   [  ]
  527927-575902 |                                                   [  ]
  479952-527927 |                                                   [  ]
  431977-479952 |                                                   [  ]
  384002-431977 |                                                   [ 1 ]
  336026-384001 |                                                   [ 3 ]
  288051-336026 |                                                   [ 6 ]
  240076-288051 |                                                   [ 13 ]
  192101-240076 |                                                   [ 16 ]
  144125-192100 |                                                   [ 34 ]
  96150-144125  |                                                   [ 56 ]
  48175-96150   |                                                   [ 104 ]
  200-48175     |************************************************** [ 7670 ]

Storage Throughput = excellent ( 1106.06 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37946754 bp ( 37927042 non ambiguous )
   - Num Contigs Represented = 7904
   - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 291 raw families identified
   - RepeatScout: Running filtering stage.. 280 families remaining
   - RepeatScout: 00:01:31 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 273 families... 00:00:40 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 23 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:02:25 (hh:mm:ss) Elapsed Time : 250 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 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2935 repeats masked totaling 539204 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10039670 bp
       Num Contigs Represented = 2147
       Non ambiguous bp:
             Initial: 10034280 bp
             After Masking: 9421360 bp
             Masked: 6.11 % 
 -- Input Database Coverage: 10039670 bp out of 37946850 bp ( 26.46 % )
Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2478651
Comparison Time: 00:12:10 (hh:mm:ss) Elapsed Time, 3875 HSPs Collected
Number of families returned by RECON: 820
Round Time: 00:12:48 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       9323 repeats masked totaling 1635795 bp(s).
   - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27907037 bp
       Num Contigs Represented = 5912
       Non ambiguous bp:
             Initial: 27892715 bp
             After Masking: 26054030 bp
             Masked: 6.59 % 
 -- Input Database Coverage: 37946707 bp out of 37946850 bp ( 100.00 % )
Sampling Time: 00:00:58 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 20151726
Comparison Time: 00:45:39 (hh:mm:ss) Elapsed Time, 20604 HSPs Collected
Number of families returned by RECON: 3315
Round Time: 00:47:09 (hh:mm:ss) Elapsed Time : 38 families discovered.

RepeatScout/RECON discovery complete: 289 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.yetRhv/RM_1355960.TueSep90101482025
# 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: 00:00:42 (hh:mm:ss) Elapsed Time


Program Time: 01:03:04 (hh:mm:ss) Elapsed Time