RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.K6WQWc/RM_2509497.ThuSep110052302025
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: 1757577149
Database = /dev/shm/rModeler.K6WQWc/GCA_021655885.1_ASM2165588v1 
  - Sequences = 957
  - Bases = 33865899
  - N50 = 94584
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  537405-575756 |                                                   [ 1 ]
  499054-537404 |                                                   [  ]
  460703-499053 |                                                   [ 1 ]
  422352-460702 |                                                   [ 1 ]
  384002-422352 |                                                   [  ]
  345651-384001 |                                                   [ 1 ]
  307300-345650 |                                                   [ 3 ]
  268949-307299 |                                                   [ 4 ]
  230598-268948 |                                                   [ 4 ]
  192248-230598 |                                                   [ 7 ]
  153897-192247 |*                                                  [ 23 ]
  115546-153896 |*                                                  [ 25 ]
  77195-115545  |*****                                              [ 69 ]
  38844-77194   |*********                                          [ 133 ]
  494-38844     |************************************************** [ 685 ]

Storage Throughput = excellent ( 1637.21 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 33865741 bp ( 33864006 non ambiguous )
   - Num Contigs Represented = 957
   - 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.. : 19 raw families identified
   - RepeatScout: Running filtering stage.. 19 families remaining
   - RepeatScout: 00:00:33 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 17 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:00 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:00 (hh:mm:ss) Elapsed Time
Round Time: 00:00:40 (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...
       130 repeats masked totaling 17626 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10011984 bp
       Num Contigs Represented = 363
       Non ambiguous bp:
             Initial: 10011632 bp
             After Masking: 9980804 bp
             Masked: 0.31 % 
 -- Input Database Coverage: 10011984 bp out of 33865899 bp ( 29.56 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 98790
Comparison Time: 00:04:38 (hh:mm:ss) Elapsed Time, 1731 HSPs Collected
Number of families returned by RECON: 609
Round Time: 00:04:51 (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 : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       561 repeats masked totaling 67966 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 23853721 bp
       Num Contigs Represented = 751
       Non ambiguous bp:
             Initial: 23852338 bp
             After Masking: 23749103 bp
             Masked: 0.43 % 
 -- Input Database Coverage: 33865705 bp out of 33865899 bp ( 100.00 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 575128
Comparison Time: 00:13:41 (hh:mm:ss) Elapsed Time, 7711 HSPs Collected
Number of families returned by RECON: 2205
Round Time: 00:14:08 (hh:mm:ss) Elapsed Time : 9 families discovered.

RepeatScout/RECON discovery complete: 28 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.K6WQWc/RM_2509497.ThuSep110052302025
# 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: 00:19:45 (hh:mm:ss) Elapsed Time