RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.LImcPG/RM_22534.FriSep201652482024
Search Engine = rmblast 2.13.0+
Threads = 32
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1726876365
Database = /dev/shm/rModeler.LImcPG/GCA_000387465.2_piw_scaffolds_v1   - Sequences = 11541
  - Bases = 43199174
  - N50 = 11022
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  89826-96228 |                                                   [ 2 ]
  83424-89825 |                                                   [  ]
  77022-83423 |                                                   [ 2 ]
  70620-77021 |                                                   [  ]
  64218-70619 |                                                   [  ]
  57816-64217 |                                                   [ 3 ]
  51414-57815 |                                                   [ 7 ]
  45013-51414 |                                                   [ 12 ]
  38611-45012 |                                                   [ 18 ]
  32209-38610 |                                                   [ 42 ]
  25807-32208 |                                                   [ 100 ]
  19405-25806 |*                                                  [ 207 ]
  13003-19404 |**                                                 [ 485 ]
  6601-13002  |*****                                              [ 1061 ]
  200-6601    |************************************************** [ 9602 ]

Storage Throughput = excellent ( 1075.28 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 41472482 bp ( 40008101 non ambiguous )
   - Num Contigs Represented = 11174
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:21:55 (hh:mm:ss) Elapsed Time
Round Time: 00:24:09 (hh:mm:ss) Elapsed Time : 275 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 00:00:13 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2289 repeats masked totaling 349590 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10379937 bp
       Num Contigs Represented = 2668
       Non ambiguous bp:
             Initial: 10013847 bp
             After Masking: 9659234 bp
             Masked: 3.54 % 
 -- Input Database Coverage: 10379937 bp out of 43199174 bp ( 24.03 % )
Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 3568456
Comparison Time: 00:12:40 (hh:mm:ss) Elapsed Time, 9494 HSPs Collected
Number of families returned by RECON: 2505
Round Time: 00:13:19 (hh:mm:ss) Elapsed Time : 0 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 00:00:37 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       7009 repeats masked totaling 1129905 bp(s).
   - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 31107979 bp
       Num Contigs Represented = 8524
       Non ambiguous bp:
             Initial: 30007394 bp
             After Masking: 28862067 bp
             Masked: 3.82 % 
 -- Input Database Coverage: 41487916 bp out of 43199174 bp ( 96.04 % )
Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 36521331
Comparison Time: 00:58:58 (hh:mm:ss) Elapsed Time, 126688 HSPs Collected
Number of families returned by RECON: 11222
Round Time: 01:04:35 (hh:mm:ss) Elapsed Time : 94 families discovered.
   - Increasing sample size to include end piece now = 92819237


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 92819237 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       389 repeats masked totaling 76306 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 1711097 bp
       Num Contigs Represented = 364
       Non ambiguous bp:
             Initial: 1643399 bp
             After Masking: 1566458 bp
             Masked: 4.68 % 
 -- Input Database Coverage: 43199013 bp out of 43199174 bp ( 100.00 % )
Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 66066
Comparison Time: 00:01:28 (hh:mm:ss) Elapsed Time, 159 HSPs Collected
Number of families returned by RECON: 98
Round Time: 00:01:35 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 369 families found


Classification Time: 00:06:04 (hh:mm:ss) Elapsed Time


Program Time: 01:49:42 (hh:mm:ss) Elapsed Time