RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.TBo0CX/RM_3576629.FriSep120524282025
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: 1757679867
Database = /dev/shm/rModeler.TBo0CX/GCA_037075405.1_ASM3707540v1 
  - Sequences = 321
  - Bases = 39808360
  - N50 = 1012995
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2548931-2730962 |                                                   [ 1 ]
  2366900-2548930 |                                                   [  ]
  2184869-2366899 |                                                   [ 1 ]
  2002839-2184869 |                                                   [ 1 ]
  1820808-2002838 |                                                   [ 1 ]
  1638777-1820807 |                                                   [ 2 ]
  1456746-1638776 |                                                   [  ]
  1274716-1456746 |                                                   [ 1 ]
  1092685-1274715 |                                                   [ 4 ]
  910654-1092684  |*                                                  [ 6 ]
  728623-910653   |                                                   [ 5 ]
  546593-728623   |*                                                  [ 7 ]
  364562-546592   |                                                   [ 5 ]
  182531-364561   |                                                   [ 5 ]
  501-182531      |************************************************** [ 282 ]

Storage Throughput = excellent ( 1641.03 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39808332 bp ( 39806782 non ambiguous )
   - Num Contigs Represented = 321
   - 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.. : 28 raw families identified
   - RepeatScout: Running filtering stage.. 20 families remaining
   - RepeatScout: 00:00:40 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 18 families... 00:00:07 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 1 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:51 (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 : 00:00:01 (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...
       229 repeats masked totaling 77000 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10036109 bp
       Num Contigs Represented = 119
       Non ambiguous bp:
             Initial: 10035759 bp
             After Masking: 9942283 bp
             Masked: 0.93 % 
 -- Input Database Coverage: 10036109 bp out of 39808360 bp ( 25.21 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 50721
Comparison Time: 00:04:02 (hh:mm:ss) Elapsed Time, 1852 HSPs Collected
Number of families returned by RECON: 779
Round Time: 00:04:15 (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 : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       626 repeats masked totaling 132201 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29772143 bp
       Num Contigs Represented = 254
       Non ambiguous bp:
             Initial: 29770943 bp
             After Masking: 29591176 bp
             Masked: 0.60 % 
 -- Input Database Coverage: 39808252 bp out of 39808360 bp ( 100.00 % )
Sampling Time: 00:00:23 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 446985
Comparison Time: 00:15:50 (hh:mm:ss) Elapsed Time, 17000 HSPs Collected
Number of families returned by RECON: 3994
Round Time: 00:17:03 (hh:mm:ss) Elapsed Time : 9 families discovered.

RepeatScout/RECON discovery complete: 27 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.TBo0CX/RM_3576629.FriSep120524282025
# 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: 00:00:08 (hh:mm:ss) Elapsed Time


Program Time: 00:22:17 (hh:mm:ss) Elapsed Time