RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.kTG9r1/RM_1209.MonAug121805322024
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: 1723511131
Database = /dev/shm/rModeler.kTG9r1/GCA_000966635.1_Fus_gra_233423_v1   - Sequences = 869
  - Bases = 36490312
  - N50 = 168060
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  562021-602152 |                                                   [ 1 ]
  521891-562021 |                                                   [ 1 ]
  481761-521891 |                                                   [ 3 ]
  441631-481761 |                                                   [ 1 ]
  401501-441631 |                                                   [ 3 ]
  361371-401501 |                                                   [ 3 ]
  321241-361371 |                                                   [ 10 ]
  281110-321240 |                                                   [ 2 ]
  240980-281110 |                                                   [ 9 ]
  200850-240980 |*                                                  [ 18 ]
  160720-200850 |*                                                  [ 21 ]
  120590-160720 |**                                                 [ 38 ]
  80460-120590  |***                                                [ 50 ]
  40330-80460   |*****                                              [ 68 ]
  200-40330     |************************************************** [ 641 ]

Storage Throughput = excellent ( 1028.06 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 36490182 bp ( 36225409 non ambiguous )
   - Num Contigs Represented = 869
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:14:51 (hh:mm:ss) Elapsed Time
Round Time: 00:15:18 (hh:mm:ss) Elapsed Time : 8 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 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       371 repeats masked totaling 39170 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10106931 bp
       Num Contigs Represented = 318
       Non ambiguous bp:
             Initial: 10035739 bp
             After Masking: 9991728 bp
             Masked: 0.44 % 
 -- Input Database Coverage: 10106931 bp out of 36490312 bp ( 27.70 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 95703
Comparison Time: 00:05:22 (hh:mm:ss) Elapsed Time, 1399 HSPs Collected
Number of families returned by RECON: 584
Round Time: 00:05:39 (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 : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1021 repeats masked totaling 108349 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 26383197 bp
       Num Contigs Represented = 695
       Non ambiguous bp:
             Initial: 26189616 bp
             After Masking: 26067621 bp
             Masked: 0.47 % 
 -- Input Database Coverage: 36490128 bp out of 36490312 bp ( 100.00 % )
Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 685035
Comparison Time: 00:23:10 (hh:mm:ss) Elapsed Time, 9477 HSPs Collected
Number of families returned by RECON: 2734
Round Time: 00:24:04 (hh:mm:ss) Elapsed Time : 9 families discovered.

RepeatScout/RECON discovery complete: 17 families found


Classification Time: 00:00:08 (hh:mm:ss) Elapsed Time


Program Time: 00:45:09 (hh:mm:ss) Elapsed Time