RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.17SOvJ/RM_1410466.MonSep81608462025
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: 1757372926
Database = /dev/shm/rModeler.17SOvJ/GCA_001717915.1_ASM171791v1 
  - Sequences = 520
  - Bases = 36350275
  - N50 = 155162
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  622768-667238 |                                                   [ 1 ]
  578299-622768 |                                                   [  ]
  533830-578299 |                                                   [  ]
  489361-533830 |                                                   [  ]
  444892-489361 |                                                   [  ]
  400422-444891 |                                                   [ 3 ]
  355953-400422 |                                                   [ 2 ]
  311484-355953 |                                                   [ 2 ]
  267015-311484 |*                                                  [ 9 ]
  222546-267015 |***                                                [ 18 ]
  178076-222545 |*****                                              [ 28 ]
  133607-178076 |*******                                            [ 39 ]
  89138-133607  |*******                                            [ 43 ]
  44669-89138   |*****************                                  [ 97 ]
  200-44669     |************************************************** [ 278 ]

Storage Throughput = excellent ( 1681.92 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36350199 bp ( 36337306 non ambiguous )
   - Num Contigs Represented = 520
   - 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.. : 15 raw families identified
   - RepeatScout: Running filtering stage.. 15 families remaining
   - RepeatScout: 00:00:35 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 15 families... 00:00:04 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 3 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 : 11 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...
       139 repeats masked totaling 17875 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10038154 bp
       Num Contigs Represented = 233
       Non ambiguous bp:
             Initial: 10034751 bp
             After Masking: 10005180 bp
             Masked: 0.29 % 
 -- Input Database Coverage: 10038154 bp out of 36350275 bp ( 27.62 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 57630
Comparison Time: 00:04:17 (hh:mm:ss) Elapsed Time, 25428 HSPs Collected
Number of families returned by RECON: 872
Round Time: 00:04:39 (hh:mm:ss) Elapsed Time : 4 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...
       597 repeats masked totaling 89128 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26311997 bp
       Num Contigs Represented = 439
       Non ambiguous bp:
             Initial: 26302507 bp
             After Masking: 26185258 bp
             Masked: 0.45 % 
 -- Input Database Coverage: 36350151 bp out of 36350275 bp ( 100.00 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 392941
Comparison Time: 00:14:29 (hh:mm:ss) Elapsed Time, 194493 HSPs Collected
Number of families returned by RECON: 3491
Round Time: 00:15:44 (hh:mm:ss) Elapsed Time : 7 families discovered.

RepeatScout/RECON discovery complete: 22 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.17SOvJ/RM_1410466.MonSep81608462025
# 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: 00:21:13 (hh:mm:ss) Elapsed Time