RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.uzDzAf/RM_2782017.ThuOct300846322025
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: 1761839191
Database = /dev/shm/rModeler.uzDzAf/GCA_023079325.1_ASM2307932v1 
  - Sequences = 209
  - Bases = 25051135
  - N50 = 1259727
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1756485-1881877 |                                                   [ 1 ]
  1631093-1756484 |                                                   [ 1 ]
  1505702-1631093 |                                                   [ 1 ]
  1380310-1505701 |                                                   [ 2 ]
  1254919-1380310 |                                                   [ 3 ]
  1129527-1254918 |                                                   [ 2 ]
  1004136-1129527 |                                                   [ 2 ]
  878744-1004135  |                                                   [ 2 ]
  753353-878744   |                                                   [ 2 ]
  627961-753352   |                                                   [  ]
  502570-627961   |                                                   [ 2 ]
  377178-502569   |                                                   [ 3 ]
  251787-377178   |                                                   [ 1 ]
  126395-251786   |                                                   [ 3 ]
  1004-126395     |************************************************** [ 184 ]

Storage Throughput = excellent ( 1135.85 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 25051011 bp ( 25050705 non ambiguous )
   - Num Contigs Represented = 209
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 9 raw families identified
   - RepeatScout: Running filtering stage.. 8 families remaining
   - RepeatScout: 00:00:32 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 8 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:44 (hh:mm:ss) Elapsed Time : 8 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 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       132 repeats masked totaling 16463 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10030734 bp
       Num Contigs Represented = 101
       Non ambiguous bp:
             Initial: 10030713 bp
             After Masking: 10007635 bp
             Masked: 0.23 % 
 -- Input Database Coverage: 10030734 bp out of 25051135 bp ( 40.04 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 48828
Comparison Time: 00:05:36 (hh:mm:ss) Elapsed Time, 2161 HSPs Collected
Number of families returned by RECON: 782
Round Time: 00:06:00 (hh:mm:ss) Elapsed Time : 2 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...
       349 repeats masked totaling 44699 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 15020197 bp
       Num Contigs Represented = 140
       Non ambiguous bp:
             Initial: 15019912 bp
             After Masking: 14958525 bp
             Masked: 0.41 % 
 -- Input Database Coverage: 25050931 bp out of 25051135 bp ( 100.00 % )
Sampling Time: 00:00:23 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 114003
Comparison Time: 00:10:19 (hh:mm:ss) Elapsed Time, 3199 HSPs Collected
Number of families returned by RECON: 1317
Round Time: 00:11:03 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 11 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.uzDzAf/RM_2782017.ThuOct300846322025
# 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: 00:00:12 (hh:mm:ss) Elapsed Time


Program Time: 00:17:59 (hh:mm:ss) Elapsed Time