RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.zzb6v2/RM_3130532.TueSep92315022025
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: 1757484902
Database = /dev/shm/rModeler.zzb6v2/GCA_012922625.1_ASM1292262v1 
  - Sequences = 155
  - Bases = 19200339
  - N50 = 400153
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  846628-907028 |*                                                  [ 2 ]
  786229-846628 |                                                   [  ]
  725830-786229 |                                                   [  ]
  665430-725829 |*                                                  [ 3 ]
  605031-665430 |                                                   [ 1 ]
  544632-605031 |                                                   [ 1 ]
  484232-544631 |*                                                  [ 3 ]
  423833-484232 |**                                                 [ 4 ]
  363434-423833 |**                                                 [ 4 ]
  303034-363433 |*                                                  [ 2 ]
  242635-303034 |****                                               [ 7 ]
  182236-242635 |****                                               [ 7 ]
  121836-182235 |********                                           [ 14 ]
  61437-121836  |*************                                      [ 23 ]
  1038-61437    |************************************************** [ 84 ]

Storage Throughput = excellent ( 1668.09 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19200249 bp ( 19184859 non ambiguous )
   - Num Contigs Represented = 155
   - 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.. : 7 raw families identified
   - RepeatScout: Running filtering stage.. 7 families remaining
   - RepeatScout: 00:00:17 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 7 families... 00:00:03 (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: 00:00:23 (hh:mm:ss) Elapsed Time : 7 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...
       217 repeats masked totaling 58258 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10020374 bp
       Num Contigs Represented = 112
       Non ambiguous bp:
             Initial: 10013596 bp
             After Masking: 9938789 bp
             Masked: 0.75 % 
 -- Input Database Coverage: 10020374 bp out of 19200339 bp ( 52.19 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 45753
Comparison Time: 00:04:06 (hh:mm:ss) Elapsed Time, 987 HSPs Collected
Number of families returned by RECON: 565
Round Time: 00:04:14 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 39200339


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39200339 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...
       230 repeats masked totaling 62479 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9179821 bp
       Num Contigs Represented = 107
       Non ambiguous bp:
             Initial: 9171209 bp
             After Masking: 9091739 bp
             Masked: 0.87 % 
 -- Input Database Coverage: 19200195 bp out of 19200339 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 39340
Comparison Time: 00:03:40 (hh:mm:ss) Elapsed Time, 914 HSPs Collected
Number of families returned by RECON: 450
Round Time: 00:03:48 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 7 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.zzb6v2/RM_3130532.TueSep92315022025
# 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: 00:08:31 (hh:mm:ss) Elapsed Time