RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.WA0EAM/RM_1168456.ThuFeb121230542026
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: 1770928254
Database = /dev/shm/rModeler.WA0EAM/GCA_037892995.1_UAEM_Aspbra_1.0 
  - Sequences = 824
  - Bases = 36963273
  - N50 = 2072012
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  4243274-4546351 |                                                   [ 1 ]
  3940197-4243273 |                                                   [  ]
  3637121-3940197 |                                                   [ 2 ]
  3334044-3637120 |                                                   [  ]
  3030968-3334044 |                                                   [  ]
  2727891-3030967 |                                                   [ 1 ]
  2424814-2727890 |                                                   [  ]
  2121738-2424814 |                                                   [  ]
  1818661-2121737 |                                                   [ 3 ]
  1515585-1818661 |                                                   [ 1 ]
  1212508-1515584 |                                                   [ 4 ]
  909431-1212507  |                                                   [  ]
  606355-909431   |                                                   [ 6 ]
  303278-606354   |                                                   [ 3 ]
  202-303278      |************************************************** [ 803 ]

Storage Throughput = excellent ( 1678.13 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36963202 bp ( 36951496 non ambiguous )
   - Num Contigs Represented = 824
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 87 raw families identified
   - RepeatScout: Running filtering stage.. 51 families remaining
   - RepeatScout: 00:00:43 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 48 families... 00:00:07 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:55 (hh:mm:ss) Elapsed Time : 46 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 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       359 repeats masked totaling 114836 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10024034 bp
       Num Contigs Represented = 259
       Non ambiguous bp:
             Initial: 10021706 bp
             After Masking: 9880558 bp
             Masked: 1.41 % 
 -- Input Database Coverage: 10024034 bp out of 36963273 bp ( 27.12 % )
Sampling Time: 00:00:14 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 110685
Comparison Time: 00:05:37 (hh:mm:ss) Elapsed Time, 3348 HSPs Collected
Number of families returned by RECON: 667
Round Time: 00:27:47 (hh:mm:ss) Elapsed Time : 5 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 00:00:23 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1248 repeats masked totaling 689801 bp(s).
   - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26939088 bp
       Num Contigs Represented = 594
       Non ambiguous bp:
             Initial: 26929710 bp
             After Masking: 26176254 bp
             Masked: 2.80 % 
 -- Input Database Coverage: 36963122 bp out of 36963273 bp ( 100.00 % )
Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 732655
Comparison Time: 00:15:39 (hh:mm:ss) Elapsed Time, 16302 HSPs Collected
Number of families returned by RECON: 2875
Round Time: 00:22:20 (hh:mm:ss) Elapsed Time : 12 families discovered.

RepeatScout/RECON discovery complete: 63 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.WA0EAM/RM_1168456.ThuFeb121230542026
# 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: 00:00:20 (hh:mm:ss) Elapsed Time


Program Time: 00:51:22 (hh:mm:ss) Elapsed Time