RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.2W1o5r/RM_3246875.TueSep92310302025
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: 1757484629
Database = /dev/shm/rModeler.2W1o5r/GCA_012922615.1_ASM1292261v1 
  - Sequences = 128
  - Bases = 19020389
  - N50 = 491916
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1187073-1271788 |                                                   [ 1 ]
  1102359-1187073 |                                                   [  ]
  1017645-1102359 |                                                   [  ]
  932930-1017644  |                                                   [  ]
  848216-932930   |**                                                 [ 4 ]
  763502-848216   |                                                   [  ]
  678788-763502   |                                                   [ 1 ]
  594073-678787   |**                                                 [ 3 ]
  509359-594073   |*                                                  [ 2 ]
  424645-509359   |**                                                 [ 4 ]
  339931-424645   |**                                                 [ 3 ]
  255216-339930   |******                                             [ 9 ]
  170502-255216   |**                                                 [ 4 ]
  85788-170502    |**************                                     [ 22 ]
  1074-85788      |************************************************** [ 75 ]

Storage Throughput = excellent ( 1645.31 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 19020229 bp ( 19006888 non ambiguous )
   - Num Contigs Represented = 128
   - 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.. : 6 raw families identified
   - RepeatScout: Running filtering stage.. 6 families remaining
   - RepeatScout: 00:00:16 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 6 families... 00:00:03 (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: 00:00:23 (hh:mm:ss) Elapsed Time : 6 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 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       200 repeats masked totaling 55446 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10021702 bp
       Num Contigs Represented = 91
       Non ambiguous bp:
             Initial: 10014414 bp
             After Masking: 9939462 bp
             Masked: 0.75 % 
 -- Input Database Coverage: 10021702 bp out of 19020389 bp ( 52.69 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 42778
Comparison Time: 00:04:00 (hh:mm:ss) Elapsed Time, 1021 HSPs Collected
Number of families returned by RECON: 537
Round Time: 00:04:08 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 39020389


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 39020389 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       218 repeats masked totaling 58102 bp(s).
   - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8998447 bp
       Num Contigs Represented = 90
       Non ambiguous bp:
             Initial: 8992394 bp
             After Masking: 8919686 bp
             Masked: 0.81 % 
 -- Input Database Coverage: 19020149 bp out of 19020389 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 35511
Comparison Time: 00:03:37 (hh:mm:ss) Elapsed Time, 809 HSPs Collected
Number of families returned by RECON: 436
Round Time: 00:03:46 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 6 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.2W1o5r/RM_3246875.TueSep92310302025
# 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: 00:08:22 (hh:mm:ss) Elapsed Time