RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.OMcLPr/RM_31563.MonAug121457172024
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: 1723499836
Database = /dev/shm/rModeler.OMcLPr/GCA_000239835.2_Akaw_assembly01   - Sequences = 1160
  - Bases = 37112601
  - N50 = 934240
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  1938944-2077433 |                                                   [ 2 ]
  1800455-1938943 |                                                   [  ]
  1661966-1800454 |                                                   [  ]
  1523477-1661965 |                                                   [ 3 ]
  1384988-1523476 |                                                   [ 2 ]
  1246499-1384987 |                                                   [  ]
  1108010-1246498 |                                                   [ 1 ]
  969522-1108010  |                                                   [ 2 ]
  831033-969521   |                                                   [ 4 ]
  692544-831032   |                                                   [ 3 ]
  554055-692543   |                                                   [ 5 ]
  415566-554054   |                                                   [ 9 ]
  277077-415565   |                                                   [ 6 ]
  138588-277076   |                                                   [ 12 ]
  100-138588      |************************************************** [ 1111 ]

Storage Throughput = excellent ( 1047.86 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37112482 bp ( 36874421 non ambiguous )
   - Num Contigs Represented = 1160
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:14:16 (hh:mm:ss) Elapsed Time
Round Time: 00:15:25 (hh:mm:ss) Elapsed Time : 48 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 00:00:16 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       356 repeats masked totaling 88346 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10098095 bp
       Num Contigs Represented = 341
       Non ambiguous bp:
             Initial: 10032596 bp
             After Masking: 9924990 bp
             Masked: 1.07 % 
 -- Input Database Coverage: 10098095 bp out of 37112601 bp ( 27.21 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 140715
Comparison Time: 00:07:13 (hh:mm:ss) Elapsed Time, 1952 HSPs Collected
Number of families returned by RECON: 733
Round Time: 00:10:28 (hh:mm:ss) Elapsed Time : 1 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 00:00:44 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1070 repeats masked totaling 303013 bp(s).
   - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27014307 bp
       Num Contigs Represented = 877
       Non ambiguous bp:
             Initial: 26841745 bp
             After Masking: 26484399 bp
             Masked: 1.33 % 
 -- Input Database Coverage: 37112402 bp out of 37112601 bp ( 100.00 % )
Sampling Time: 00:01:02 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1072380
Comparison Time: 00:37:10 (hh:mm:ss) Elapsed Time, 15616 HSPs Collected
Number of families returned by RECON: 2863
Round Time: 01:20:59 (hh:mm:ss) Elapsed Time : 12 families discovered.

RepeatScout/RECON discovery complete: 61 families found


Classification Time: 00:05:33 (hh:mm:ss) Elapsed Time


Program Time: 01:52:25 (hh:mm:ss) Elapsed Time