RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.4u4Swh/RM_654019.WedSep101426222025
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: 1757539582
Database = /dev/shm/rModeler.4u4Swh/GCA_018154835.1_ASM1815483v1 
  - Sequences = 354
  - Bases = 19572093
  - N50 = 551102
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1741252-1865613 |                                                   [ 1 ]
  1616891-1741251 |                                                   [  ]
  1492530-1616890 |                                                   [  ]
  1368169-1492529 |                                                   [  ]
  1243808-1368168 |                                                   [  ]
  1119447-1243807 |                                                   [  ]
  995086-1119446  |                                                   [ 4 ]
  870726-995086   |                                                   [ 1 ]
  746365-870725   |                                                   [  ]
  622004-746364   |                                                   [ 2 ]
  497643-622003   |                                                   [ 4 ]
  373282-497642   |*                                                  [ 7 ]
  248921-373281   |*                                                  [ 8 ]
  124560-248920   |**                                                 [ 13 ]
  200-124560      |************************************************** [ 314 ]

Storage Throughput = excellent ( 1608.60 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19571995 bp ( 19568958 non ambiguous )
   - Num Contigs Represented = 354
   - 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.. : 28 raw families identified
   - RepeatScout: Running filtering stage.. 28 families remaining
   - RepeatScout: 00:00:26 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 24 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: 00:00:34 (hh:mm:ss) Elapsed Time : 20 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...
       288 repeats masked totaling 52482 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10029620 bp
       Num Contigs Represented = 181
       Non ambiguous bp:
             Initial: 10028501 bp
             After Masking: 9924627 bp
             Masked: 1.04 % 
 -- Input Database Coverage: 10029620 bp out of 19572093 bp ( 51.24 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 78210
Comparison Time: 00:04:36 (hh:mm:ss) Elapsed Time, 19616 HSPs Collected
Number of families returned by RECON: 1612
Round Time: 00:05:12 (hh:mm:ss) Elapsed Time : 6 families discovered.
   - Increasing sample size to include end piece now = 39572093


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39572093 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...
       2346 repeats masked totaling 273186 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9542295 bp
       Num Contigs Represented = 216
       Non ambiguous bp:
             Initial: 9540377 bp
             After Masking: 9215505 bp
             Masked: 3.41 % 
 -- Input Database Coverage: 19571915 bp out of 19572093 bp ( 100.00 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 85491
Comparison Time: 00:04:31 (hh:mm:ss) Elapsed Time, 2715 HSPs Collected
Number of families returned by RECON: 729
Round Time: 00:04:46 (hh:mm:ss) Elapsed Time : 3 families discovered.

RepeatScout/RECON discovery complete: 29 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.4u4Swh/RM_654019.WedSep101426222025
# 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: 00:00:07 (hh:mm:ss) Elapsed Time


Program Time: 00:10:39 (hh:mm:ss) Elapsed Time