RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.jAs57f/RM_73489.MonFeb202046272023
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: 1676954785
Database = /dev/shm/rModeler.jAs57f/GCF_000209065.1_ASM20906v1   - Sequences = 29495
  - Bases = 89937456
  - N50 = 88821
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  924679-990720 |                                                   [ 1 ]
  858639-924679 |                                                   [  ]
  792598-858638 |                                                   [ 3 ]
  726558-792598 |                                                   [  ]
  660518-726558 |                                                   [ 1 ]
  594477-660517 |                                                   [ 1 ]
  528437-594477 |                                                   [ 3 ]
  462396-528436 |                                                   [ 3 ]
  396356-462396 |                                                   [ 9 ]
  330316-396356 |                                                   [ 6 ]
  264275-330315 |                                                   [ 21 ]
  198235-264275 |                                                   [ 39 ]
  132194-198234 |                                                   [ 48 ]
  66154-132194  |                                                   [ 127 ]
  114-66154     |************************************************** [ 29233 ]

Storage Throughput = excellent ( 1342.04 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40156636 bp ( 40014856 non ambiguous )
   - Num Contigs Represented = 13086
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:10:44 (hh:mm:ss) Elapsed Time
Round Time: 03:08:19 (hh:mm:ss) Elapsed Time : 387 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6915 repeats masked totaling 4702006 bp(s).
   - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10035258 bp
       Num Contigs Represented = 3422
       Non ambiguous bp:
             Initial: 10000358 bp
             After Masking: 4571026 bp
             Masked: 54.29 % 
 -- Input Database Coverage: 10035258 bp out of 89937456 bp ( 11.16 % )
Sampling Time: 00:00:48 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 6004845
Comparison Time: 00:25:22 (hh:mm:ss) Elapsed Time, 2509 HSPs Collected
Number of families returned by RECON: 664
Round Time: 00:26:24 (hh:mm:ss) Elapsed Time : 2 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 00:01:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       21336 repeats masked totaling 14544681 bp(s).
   - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30121330 bp
       Num Contigs Represented = 9759
       Non ambiguous bp:
             Initial: 30014450 bp
             After Masking: 13337425 bp
             Masked: 55.56 % 
 -- Input Database Coverage: 40156588 bp out of 89937456 bp ( 44.65 % )
Sampling Time: 00:02:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 50235276
Comparison Time: 01:24:02 (hh:mm:ss) Elapsed Time, 19050 HSPs Collected
Number of families returned by RECON: 2568
Round Time: 01:28:10 (hh:mm:ss) Elapsed Time : 14 families discovered.


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 90000000 bp
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:48 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       38134 repeats masked totaling 24443613 bp(s).
   - TE Masking time 00:01:56 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 49780703 bp
       Num Contigs Represented = 16664
       Non ambiguous bp:
             Initial: 49597383 bp
             After Masking: 21522956 bp
             Masked: 56.60 % 
 -- Input Database Coverage: 89937291 bp out of 89937456 bp ( 100.00 % )
Sampling Time: 00:03:53 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 147825415
Comparison Time: 02:30:24 (hh:mm:ss) Elapsed Time, 32603 HSPs Collected
Number of families returned by RECON: 4154
Round Time: 02:37:43 (hh:mm:ss) Elapsed Time : 35 families discovered.

RepeatScout/RECON discovery complete: 438 families found


Classification Time: 00:37:00 (hh:mm:ss) Elapsed Time


Program Time: 08:17:36 (hh:mm:ss) Elapsed Time