RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.ro1L94/RM_2706.MonAug121621032024
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: 1723504862
Database = /dev/shm/rModeler.ro1L94/GCA_000401635.1_Muco_sp_1006Ph_V1   - Sequences = 470
  - Bases = 36348485
  - N50 = 141765
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  620054-664271 |                                                   [ 1 ]
  575837-620053 |                                                   [  ]
  531620-575836 |                                                   [  ]
  487403-531619 |                                                   [  ]
  443187-487403 |                                                   [ 1 ]
  398970-443186 |                                                   [ 1 ]
  354753-398969 |                                                   [ 4 ]
  310536-354752 |                                                   [ 4 ]
  266319-310535 |*                                                  [ 5 ]
  222103-266319 |***                                                [ 14 ]
  177886-222102 |****                                               [ 21 ]
  133669-177885 |*********                                          [ 40 ]
  89452-133668  |****************                                   [ 70 ]
  45235-89451   |*********************                              [ 93 ]
  1019-45235    |************************************************** [ 216 ]

Storage Throughput = excellent ( 1046.10 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36348381 bp ( 34134512 non ambiguous )
   - Num Contigs Represented = 470
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:14:50 (hh:mm:ss) Elapsed Time
Round Time: 00:19:20 (hh:mm:ss) Elapsed Time : 221 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 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       4532 repeats masked totaling 1370873 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10606450 bp
       Num Contigs Represented = 244
       Non ambiguous bp:
             Initial: 10006605 bp
             After Masking: 8611576 bp
             Masked: 13.94 % 
 -- Input Database Coverage: 10606450 bp out of 36348485 bp ( 29.18 % )
Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 61776
Comparison Time: 00:06:24 (hh:mm:ss) Elapsed Time, 3902 HSPs Collected
Number of families returned by RECON: 1394
Round Time: 00:07:01 (hh:mm:ss) Elapsed Time : 7 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       11597 repeats masked totaling 3438938 bp(s).
   - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 25741867 bp
       Num Contigs Represented = 400
       Non ambiguous bp:
             Initial: 24127843 bp
             After Masking: 20621517 bp
             Masked: 14.53 % 
 -- Input Database Coverage: 36348317 bp out of 36348485 bp ( 100.00 % )
Sampling Time: 00:00:58 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 352380
Comparison Time: 00:25:28 (hh:mm:ss) Elapsed Time, 19059 HSPs Collected
Number of families returned by RECON: 4819
Round Time: 00:27:23 (hh:mm:ss) Elapsed Time : 14 families discovered.

RepeatScout/RECON discovery complete: 242 families found


Classification Time: 00:09:55 (hh:mm:ss) Elapsed Time


Program Time: 01:03:39 (hh:mm:ss) Elapsed Time