RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.vIzqkm/RM_2025827.TueSep90049592025
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: 1757404198
Database = /dev/shm/rModeler.vIzqkm/GCA_003690945.1_ASM369094v1 
  - Sequences = 5878
  - Bases = 38149974
  - N50 = 143549
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  451481-483716 |                                                   [ 2 ]
  419247-451481 |                                                   [ 1 ]
  387012-419246 |                                                   [ 1 ]
  354778-387012 |                                                   [ 4 ]
  322544-354778 |                                                   [ 9 ]
  290309-322543 |                                                   [ 5 ]
  258075-290309 |                                                   [ 5 ]
  225840-258074 |                                                   [ 12 ]
  193606-225840 |                                                   [ 13 ]
  161372-193606 |                                                   [ 15 ]
  129137-161371 |                                                   [ 25 ]
  96903-129137  |                                                   [ 42 ]
  64668-96902   |                                                   [ 50 ]
  32434-64668   |                                                   [ 82 ]
  200-32434     |************************************************** [ 5612 ]

Storage Throughput = excellent ( 1110.25 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 38149854 bp ( 38086281 non ambiguous )
   - Num Contigs Represented = 5878
   - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 249 raw families identified
   - RepeatScout: Running filtering stage.. 239 families remaining
   - RepeatScout: 00:01:29 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 233 families... 00:00:37 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 29 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:02:19 (hh:mm:ss) Elapsed Time : 204 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (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...
       2452 repeats masked totaling 487249 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10056158 bp
       Num Contigs Represented = 1662
       Non ambiguous bp:
             Initial: 10040271 bp
             After Masking: 9473420 bp
             Masked: 5.65 % 
 -- Input Database Coverage: 10056158 bp out of 38149974 bp ( 26.36 % )
Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1540890
Comparison Time: 00:10:35 (hh:mm:ss) Elapsed Time, 5056 HSPs Collected
Number of families returned by RECON: 908
Round Time: 00:11:15 (hh:mm:ss) Elapsed Time : 7 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       8452 repeats masked totaling 1519729 bp(s).
   - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 28093658 bp
       Num Contigs Represented = 4367
       Non ambiguous bp:
             Initial: 28045972 bp
             After Masking: 26330727 bp
             Masked: 6.12 % 
 -- Input Database Coverage: 38149816 bp out of 38149974 bp ( 100.00 % )
Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 11705541
Comparison Time: 00:40:50 (hh:mm:ss) Elapsed Time, 20046 HSPs Collected
Number of families returned by RECON: 3217
Round Time: 00:42:35 (hh:mm:ss) Elapsed Time : 41 families discovered.

RepeatScout/RECON discovery complete: 252 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.vIzqkm/RM_2025827.TueSep90049592025
# 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: 00:00:43 (hh:mm:ss) Elapsed Time


Program Time: 00:56:52 (hh:mm:ss) Elapsed Time