RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.TS2SuS/RM_603342.WedSep101353502025
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: 1757537629
Database = /dev/shm/rModeler.TS2SuS/GCA_018153955.1_ASM1815395v1 
  - Sequences = 365
  - Bases = 19553394
  - N50 = 521356
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1743247-1867751 |                                                   [ 1 ]
  1618744-1743247 |                                                   [  ]
  1494240-1618743 |                                                   [  ]
  1369737-1494240 |                                                   [  ]
  1245234-1369737 |                                                   [  ]
  1120730-1245233 |                                                   [  ]
  996227-1120730  |                                                   [ 3 ]
  871723-996226   |                                                   [ 1 ]
  747220-871723   |                                                   [ 1 ]
  622717-747220   |                                                   [ 1 ]
  498213-622716   |                                                   [ 5 ]
  373710-498213   |                                                   [ 5 ]
  249206-373709   |*                                                  [ 9 ]
  124703-249206   |**                                                 [ 16 ]
  200-124703      |************************************************** [ 323 ]

Storage Throughput = excellent ( 1680.54 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19553241 bp ( 19546880 non ambiguous )
   - Num Contigs Represented = 365
   - 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.. : 22 raw families identified
   - RepeatScout: Running filtering stage.. 22 families remaining
   - RepeatScout: 00:00:27 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 21 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 4 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:34 (hh:mm:ss) Elapsed Time : 17 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       280 repeats masked totaling 47005 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10023312 bp
       Num Contigs Represented = 232
       Non ambiguous bp:
             Initial: 10020413 bp
             After Masking: 9923111 bp
             Masked: 0.97 % 
 -- Input Database Coverage: 10023312 bp out of 19553394 bp ( 51.26 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 96141
Comparison Time: 00:04:56 (hh:mm:ss) Elapsed Time, 17033 HSPs Collected
Number of families returned by RECON: 1569
Round Time: 00:05:29 (hh:mm:ss) Elapsed Time : 7 families discovered.
   - Increasing sample size to include end piece now = 39553394


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39553394 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2578 repeats masked totaling 258689 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9529849 bp
       Num Contigs Represented = 181
       Non ambiguous bp:
             Initial: 9526387 bp
             After Masking: 9212982 bp
             Masked: 3.29 % 
 -- Input Database Coverage: 19553161 bp out of 19553394 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 70500
Comparison Time: 00:04:25 (hh:mm:ss) Elapsed Time, 2778 HSPs Collected
Number of families returned by RECON: 743
Round Time: 00:04:38 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 25 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.TS2SuS/RM_603342.WedSep101353502025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:10:47 (hh:mm:ss) Elapsed Time