RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.NsyZ98/RM_100443.TueSep92302182025
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: 1757484138
Database = /dev/shm/rModeler.NsyZ98/GCA_012922605.1_ASM1292260v1 
  - Sequences = 128
  - Bases = 19422953
  - N50 = 509216
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1091315-1169194 |*                                                  [ 2 ]
  1013437-1091315 |                                                   [  ]
  935558-1013436  |                                                   [ 1 ]
  857680-935558   |*                                                  [ 2 ]
  779802-857680   |*                                                  [ 2 ]
  701923-779801   |                                                   [ 1 ]
  624045-701923   |                                                   [ 1 ]
  546166-624044   |*                                                  [ 2 ]
  468288-546166   |*                                                  [ 3 ]
  390410-468288   |***                                                [ 5 ]
  312531-390409   |***                                                [ 5 ]
  234653-312531   |***                                                [ 5 ]
  156774-234652   |***                                                [ 5 ]
  78896-156774    |********                                           [ 14 ]
  1018-78896      |************************************************** [ 80 ]

Storage Throughput = excellent ( 1103.69 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19422909 bp ( 19418327 non ambiguous )
   - Num Contigs Represented = 128
   - 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.. : 14 raw families identified
   - RepeatScout: Running filtering stage.. 14 families remaining
   - RepeatScout: 00:00:25 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 14 families... 00:00:06 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:38 (hh:mm:ss) Elapsed Time : 12 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...
       167 repeats masked totaling 44847 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10034444 bp
       Num Contigs Represented = 86
       Non ambiguous bp:
             Initial: 10032462 bp
             After Masking: 9966180 bp
             Masked: 0.66 % 
 -- Input Database Coverage: 10034444 bp out of 19422953 bp ( 51.66 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 41041
Comparison Time: 00:05:56 (hh:mm:ss) Elapsed Time, 2509 HSPs Collected
Number of families returned by RECON: 527
Round Time: 00:06:13 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 39422953


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39422953 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       183 repeats masked totaling 43705 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 9388399 bp
       Num Contigs Represented = 92
       Non ambiguous bp:
             Initial: 9385799 bp
             After Masking: 9322339 bp
             Masked: 0.68 % 
 -- Input Database Coverage: 19422843 bp out of 19422953 bp ( 100.00 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 39903
Comparison Time: 00:05:25 (hh:mm:ss) Elapsed Time, 5467 HSPs Collected
Number of families returned by RECON: 484
Round Time: 00:05:59 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 14 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.NsyZ98/RM_100443.TueSep92302182025
# 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: 00:00:11 (hh:mm:ss) Elapsed Time


Program Time: 00:13:01 (hh:mm:ss) Elapsed Time