RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.UJyTDh/RM_1914675.MonSep81246462025
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: 1757360806
Database = /dev/shm/rModeler.UJyTDh/GCA_000836455.1_Cryp_gatt_99_473_V1 
  - Sequences = 105
  - Bases = 17403577
  - N50 = 540065
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  853904-914829 |                                                   [ 1 ]
  792980-853904 |*                                                  [ 2 ]
  732056-792980 |                                                   [ 1 ]
  671132-732056 |*                                                  [ 2 ]
  610208-671132 |                                                   [ 1 ]
  549284-610208 |***                                                [ 4 ]
  488360-549284 |****                                               [ 5 ]
  427436-488360 |                                                   [ 1 ]
  366512-427436 |**                                                 [ 3 ]
  305588-366512 |**                                                 [ 3 ]
  244664-305588 |                                                   [ 1 ]
  183740-244664 |**                                                 [ 3 ]
  122816-183740 |************                                       [ 14 ]
  61892-122816  |******                                             [ 7 ]
  968-61892     |************************************************** [ 57 ]

Storage Throughput = excellent ( 1668.35 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 17403467 bp ( 17344390 non ambiguous )
   - Num Contigs Represented = 105
   - 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.. : 11 raw families identified
   - RepeatScout: Running filtering stage.. 10 families remaining
   - RepeatScout: 00:00:14 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 10 families... 00:00:04 (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: 00:00:21 (hh:mm:ss) Elapsed Time : 10 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       233 repeats masked totaling 50426 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10078071 bp
       Num Contigs Represented = 83
       Non ambiguous bp:
             Initial: 10032818 bp
             After Masking: 9967269 bp
             Masked: 0.65 % 
 -- Input Database Coverage: 10078071 bp out of 17403577 bp ( 57.91 % )
Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 41328
Comparison Time: 00:03:45 (hh:mm:ss) Elapsed Time, 1612 HSPs Collected
Number of families returned by RECON: 608
Round Time: 00:04:00 (hh:mm:ss) Elapsed Time : 2 families discovered.
   - Increasing sample size to include end piece now = 37403577


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 37403577 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       177 repeats masked totaling 34660 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 7325316 bp
       Num Contigs Represented = 73
       Non ambiguous bp:
             Initial: 7311492 bp
             After Masking: 7266422 bp
             Masked: 0.62 % 
 -- Input Database Coverage: 17403387 bp out of 17403577 bp ( 100.00 % )
Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 24090
Comparison Time: 00:02:39 (hh:mm:ss) Elapsed Time, 712 HSPs Collected
Number of families returned by RECON: 350
Round Time: 00:02:46 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 12 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.UJyTDh/RM_1914675.MonSep81246462025
# 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: 00:00:05 (hh:mm:ss) Elapsed Time


Program Time: 00:07:12 (hh:mm:ss) Elapsed Time