RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.JbIU7o/RM_475366.TueSep91748472025
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: 1757465326
Database = /dev/shm/rModeler.JbIU7o/GCA_011763475.1_ASM1176347v1 
  - Sequences = 3651
  - Bases = 25380879
  - N50 = 35653
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  242106-259386 |                                                   [ 1 ]
  224827-242106 |                                                   [  ]
  207548-224827 |                                                   [  ]
  190269-207548 |                                                   [ 1 ]
  172990-190269 |                                                   [ 2 ]
  155711-172990 |                                                   [ 1 ]
  138432-155711 |                                                   [ 1 ]
  121153-138432 |                                                   [  ]
  103874-121153 |                                                   [ 10 ]
  86595-103874  |                                                   [ 7 ]
  69316-86595   |                                                   [ 32 ]
  52037-69316   |                                                   [ 42 ]
  34758-52037   |*                                                  [ 122 ]
  17479-34758   |***                                                [ 252 ]
  200-17479     |************************************************** [ 3180 ]

Storage Throughput = excellent ( 1159.60 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 25380813 bp ( 25378786 non ambiguous )
   - Num Contigs Represented = 3651
   - 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.. : 263 raw families identified
   - RepeatScout: Running filtering stage.. 258 families remaining
   - RepeatScout: 00:02:06 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 255 families... 00:00:40 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 59 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time
Round Time: 00:02:55 (hh:mm:ss) Elapsed Time : 196 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 00:00:16 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3934 repeats masked totaling 999279 bp(s).
   - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10000750 bp
       Num Contigs Represented = 1446
       Non ambiguous bp:
             Initial: 10000340 bp
             After Masking: 8970375 bp
             Masked: 10.30 % 
 -- Input Database Coverage: 10000750 bp out of 25380879 bp ( 39.40 % )
Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1116765
Comparison Time: 00:12:14 (hh:mm:ss) Elapsed Time, 19896 HSPs Collected
Number of families returned by RECON: 1945
Round Time: 00:13:16 (hh:mm:ss) Elapsed Time : 16 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 00:00:26 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6920 repeats masked totaling 1649042 bp(s).
   - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 15379992 bp
       Num Contigs Represented = 2292
       Non ambiguous bp:
             Initial: 15378375 bp
             After Masking: 13679553 bp
             Masked: 11.05 % 
 -- Input Database Coverage: 25380742 bp out of 25380879 bp ( 100.00 % )
Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2838153
Comparison Time: 00:22:41 (hh:mm:ss) Elapsed Time, 13036 HSPs Collected
Number of families returned by RECON: 3221
Round Time: 00:24:03 (hh:mm:ss) Elapsed Time : 18 families discovered.

RepeatScout/RECON discovery complete: 230 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.JbIU7o/RM_475366.TueSep91748472025
# 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: 00:01:01 (hh:mm:ss) Elapsed Time


Program Time: 00:41:15 (hh:mm:ss) Elapsed Time