RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.mkCskX/RM_430117.WedSep101409162025
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: 1757538556
Database = /dev/shm/rModeler.mkCskX/GCA_018154385.1_ASM1815438v1 
  - Sequences = 353
  - Bases = 19536400
  - N50 = 469165
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1469208-1574138 |                                                   [ 1 ]
  1364279-1469208 |                                                   [  ]
  1259350-1364279 |                                                   [  ]
  1154421-1259350 |                                                   [ 1 ]
  1049492-1154421 |                                                   [  ]
  944562-1049491  |                                                   [ 1 ]
  839633-944562   |                                                   [ 1 ]
  734704-839633   |                                                   [  ]
  629775-734704   |                                                   [ 1 ]
  524846-629775   |                                                   [ 4 ]
  419916-524845   |*                                                  [ 9 ]
  314987-419916   |                                                   [ 4 ]
  210058-314987   |**                                                 [ 13 ]
  105129-210058   |*                                                  [ 12 ]
  200-105129      |************************************************** [ 306 ]

Storage Throughput = excellent ( 1668.94 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19536290 bp ( 19528724 non ambiguous )
   - Num Contigs Represented = 353
   - 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.. : 25 raw families identified
   - RepeatScout: Running filtering stage.. 25 families remaining
   - RepeatScout: 00:00:27 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 22 families... 00:00:05 (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: 00:00:35 (hh:mm:ss) Elapsed Time : 18 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       295 repeats masked totaling 54313 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10039051 bp
       Num Contigs Represented = 201
       Non ambiguous bp:
             Initial: 10034742 bp
             After Masking: 9922157 bp
             Masked: 1.12 % 
 -- Input Database Coverage: 10039051 bp out of 19536400 bp ( 51.39 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 80200
Comparison Time: 00:04:45 (hh:mm:ss) Elapsed Time, 17400 HSPs Collected
Number of families returned by RECON: 1545
Round Time: 00:05:23 (hh:mm:ss) Elapsed Time : 8 families discovered.
   - Increasing sample size to include end piece now = 39536400


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39536400 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...
       2914 repeats masked totaling 285709 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9497159 bp
       Num Contigs Represented = 206
       Non ambiguous bp:
             Initial: 9493902 bp
             After Masking: 9157646 bp
             Masked: 3.54 % 
 -- Input Database Coverage: 19536210 bp out of 19536400 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 78606
Comparison Time: 00:04:30 (hh:mm:ss) Elapsed Time, 2393 HSPs Collected
Number of families returned by RECON: 767
Round Time: 00:04:39 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 26 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.mkCskX/RM_430117.WedSep101409162025
# 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: 00:10:43 (hh:mm:ss) Elapsed Time