RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.5YeMcR/RM_3054910.MonSep81016282025
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: 1757351787
Database = /dev/shm/rModeler.5YeMcR/GCA_000149585.1_ASM14958v1 
  - Sequences = 280
  - Bases = 33030326
  - N50 = 2955614
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  6853765-7343276 |                                                   [ 1 ]
  6364255-6853765 |                                                   [  ]
  5874744-6364254 |                                                   [  ]
  5385234-5874744 |                                                   [  ]
  4895724-5385234 |                                                   [  ]
  4406213-4895723 |                                                   [  ]
  3916703-4406213 |                                                   [  ]
  3427192-3916702 |                                                   [ 1 ]
  2937682-3427192 |                                                   [ 1 ]
  2448172-2937682 |                                                   [ 2 ]
  1958661-2448171 |                                                   [ 2 ]
  1469151-1958661 |                                                   [ 1 ]
  979640-1469150  |                                                   [ 3 ]
  490130-979640   |                                                   [ 1 ]
  620-490130      |************************************************** [ 268 ]

Storage Throughput = excellent ( 1531.82 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 33030257 bp ( 30649244 non ambiguous )
   - Num Contigs Represented = 280
   - 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.. : 254 raw families identified
   - RepeatScout: Running filtering stage.. 248 families remaining
   - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 246 families... 00:01:10 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 satellite(s), 68 contained, found in 00:00:05 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:05 (hh:mm:ss) Elapsed Time
Round Time: 00:02:23 (hh:mm:ss) Elapsed Time : 178 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 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3218 repeats masked totaling 1611599 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10789077 bp
       Num Contigs Represented = 103
       Non ambiguous bp:
             Initial: 10027591 bp
             After Masking: 8358932 bp
             Masked: 16.64 % 
 -- Input Database Coverage: 10789077 bp out of 33030326 bp ( 32.66 % )
Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 61075
Comparison Time: 00:04:52 (hh:mm:ss) Elapsed Time, 3488 HSPs Collected
Number of families returned by RECON: 708
Round Time: 00:05:16 (hh:mm:ss) Elapsed Time : 3 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...
       6791 repeats masked totaling 3511368 bp(s).
   - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 22241100 bp
       Num Contigs Represented = 196
       Non ambiguous bp:
             Initial: 20621573 bp
             After Masking: 16995667 bp
             Masked: 17.58 % 
 -- Input Database Coverage: 33030177 bp out of 33030326 bp ( 100.00 % )
Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 262450
Comparison Time: 00:11:54 (hh:mm:ss) Elapsed Time, 10225 HSPs Collected
Number of families returned by RECON: 1825
Round Time: 00:12:33 (hh:mm:ss) Elapsed Time : 17 families discovered.

RepeatScout/RECON discovery complete: 198 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.5YeMcR/RM_3054910.MonSep81016282025
# 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: 00:00:41 (hh:mm:ss) Elapsed Time


Program Time: 00:20:53 (hh:mm:ss) Elapsed Time