RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.qa5vpQ/RM_10718.MonAug121648022024
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: 1723506481
Database = /dev/shm/rModeler.qa5vpQ/GCA_000447185.1_NapisBRLv01   - Sequences = 554
  - Bases = 8569501
  - N50 = 24546
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  144251-154531 |                                                   [ 1 ]
  133971-144250 |                                                   [  ]
  123691-133970 |                                                   [ 1 ]
  113412-123691 |                                                   [ 1 ]
  103132-113411 |                                                   [  ]
  92852-103131  |                                                   [ 5 ]
  82572-92851   |                                                   [ 3 ]
  72293-82572   |                                                   [ 5 ]
  62013-72292   |                                                   [ 5 ]
  51733-62012   |*                                                  [ 6 ]
  41453-51732   |*                                                  [ 9 ]
  31174-41453   |***                                                [ 21 ]
  20894-31173   |**********                                         [ 55 ]
  10614-20893   |******************************                     [ 168 ]
  335-10614     |*************************************************  [ 274 ]

Storage Throughput = excellent ( 1057.60 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 8569482 bp ( 8513837 non ambiguous )
   - Num Contigs Represented = 554
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:03:35 (hh:mm:ss) Elapsed Time
Round Time: 00:25:30 (hh:mm:ss) Elapsed Time : 53 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 00:01:56 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2313 repeats masked totaling 1160091 bp(s).
   - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8569482 bp
       Num Contigs Represented = 554
       Non ambiguous bp:
             Initial: 8513837 bp
             After Masking: 7220569 bp
             Masked: 15.19 % 
 -- Input Database Coverage: 8569482 bp out of 8569501 bp ( 100.00 % )
Sampling Time: 00:03:03 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 184528
Comparison Time: 08:27:10 (hh:mm:ss) Elapsed Time, 3872 HSPs Collected
Number of families returned by RECON: 658
Round Time: 09:06:49 (hh:mm:ss) Elapsed Time : 4 families discovered.

RepeatScout/RECON discovery complete: 57 families found


Classification Time: 00:06:47 (hh:mm:ss) Elapsed Time


Program Time: 09:39:06 (hh:mm:ss) Elapsed Time