RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.nBBbsc/RM_3364068.ThuSep110046302025
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: 1757576789
Database = /dev/shm/rModeler.nBBbsc/GCA_021655865.1_ASM2165586v1 
  - Sequences = 1349
  - Bases = 39023313
  - N50 = 127347
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  377316-404235 |                                                   [ 2 ]
  350398-377316 |                                                   [ 1 ]
  323479-350397 |                                                   [ 3 ]
  296561-323479 |                                                   [ 6 ]
  269643-296561 |                                                   [ 5 ]
  242724-269642 |                                                   [ 7 ]
  215806-242724 |                                                   [ 7 ]
  188887-215805 |                                                   [ 13 ]
  161969-188887 |                                                   [ 16 ]
  135051-161969 |*                                                  [ 26 ]
  108132-135050 |*                                                  [ 31 ]
  81214-108132  |**                                                 [ 44 ]
  54295-81213   |**                                                 [ 49 ]
  27377-54295   |****                                               [ 103 ]
  459-27377     |************************************************** [ 1036 ]

Storage Throughput = excellent ( 1606.00 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39023248 bp ( 39018804 non ambiguous )
   - Num Contigs Represented = 1349
   - 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.. : 47 raw families identified
   - RepeatScout: Running filtering stage.. 45 families remaining
   - RepeatScout: 00:00:43 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 42 families... 00:00:16 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 6 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:03 (hh:mm:ss) Elapsed Time : 36 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:00 (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...
       416 repeats masked totaling 155615 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10011344 bp
       Num Contigs Represented = 423
       Non ambiguous bp:
             Initial: 10010016 bp
             After Masking: 9842524 bp
             Masked: 1.67 % 
 -- Input Database Coverage: 10011344 bp out of 39023313 bp ( 25.65 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 129286
Comparison Time: 00:04:44 (hh:mm:ss) Elapsed Time, 2010 HSPs Collected
Number of families returned by RECON: 683
Round Time: 00:05:01 (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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1485 repeats masked totaling 572012 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29011879 bp
       Num Contigs Represented = 1077
       Non ambiguous bp:
             Initial: 29008763 bp
             After Masking: 28402137 bp
             Masked: 2.09 % 
 -- Input Database Coverage: 39023223 bp out of 39023313 bp ( 100.00 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1130256
Comparison Time: 00:18:19 (hh:mm:ss) Elapsed Time, 14141 HSPs Collected
Number of families returned by RECON: 3488
Round Time: 00:18:59 (hh:mm:ss) Elapsed Time : 15 families discovered.

RepeatScout/RECON discovery complete: 53 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.nBBbsc/RM_3364068.ThuSep110046302025
# 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: 00:00:10 (hh:mm:ss) Elapsed Time


Program Time: 00:25:13 (hh:mm:ss) Elapsed Time