RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.AmHsFj/RM_23615.MonSep162034532024
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: 1726544092
Database = /dev/shm/rModeler.AmHsFj/GCA_000346345.1_EHA.strHM3_v1   - Sequences = 1880
  - Bases = 13830719
  - N50 = 11253
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  84736-90753 |                                                   [ 1 ]
  78719-84735 |                                                   [  ]
  72702-78718 |                                                   [  ]
  66686-72702 |                                                   [  ]
  60669-66685 |                                                   [ 3 ]
  54652-60668 |                                                   [ 1 ]
  48635-54651 |                                                   [  ]
  42619-48635 |                                                   [ 2 ]
  36602-42618 |                                                   [ 10 ]
  30585-36601 |                                                   [ 14 ]
  24568-30584 |*                                                  [ 32 ]
  18552-24568 |***                                                [ 75 ]
  12535-18551 |******                                             [ 155 ]
  6518-12534  |*******************                                [ 439 ]
  502-6518    |************************************************** [ 1148 ]

Storage Throughput = excellent ( 1109.97 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 13830621 bp ( 13616974 non ambiguous )
   - Num Contigs Represented = 1880
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:11:51 (hh:mm:ss) Elapsed Time
Round Time: 00:12:41 (hh:mm:ss) Elapsed Time : 23 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 00:00:48 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       987 repeats masked totaling 145957 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10158846 bp
       Num Contigs Represented = 1382
       Non ambiguous bp:
             Initial: 10000523 bp
             After Masking: 9827952 bp
             Masked: 1.73 % 
 -- Input Database Coverage: 10158846 bp out of 13830719 bp ( 73.45 % )
Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 959805
Comparison Time: 00:28:56 (hh:mm:ss) Elapsed Time, 9070 HSPs Collected
Number of families returned by RECON: 1613
Round Time: 00:30:32 (hh:mm:ss) Elapsed Time : 10 families discovered.
   - Increasing sample size to include end piece now = 33830719


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 33830719 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       446 repeats masked totaling 98952 bp(s).
   - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 3671728 bp
       Num Contigs Represented = 503
       Non ambiguous bp:
             Initial: 3616404 bp
             After Masking: 3506404 bp
             Masked: 3.04 % 
 -- Input Database Coverage: 13830574 bp out of 13830719 bp ( 100.00 % )
Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 126253
Comparison Time: 00:05:02 (hh:mm:ss) Elapsed Time, 792 HSPs Collected
Number of families returned by RECON: 310
Round Time: 00:05:31 (hh:mm:ss) Elapsed Time : 1 families discovered.

RepeatScout/RECON discovery complete: 34 families found


Classification Time: 00:01:22 (hh:mm:ss) Elapsed Time


Program Time: 00:50:06 (hh:mm:ss) Elapsed Time