RepeatModeler Version 2.0.4
===========================
Using output directory = /data/tmp/rModeler.482iYp/RM_3139608.FriAug10627152025
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: 1754054834
Database = /data/tmp/rModeler.482iYp/GCA_900536275.1_CPANA_v1   - Sequences = 986
  - Bases = 79048330
  - N50 = 495709
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2507242-2686295 |                                                   [ 1 ]
  2328189-2507242 |                                                   [ 1 ]
  2149136-2328189 |                                                   [  ]
  1970083-2149136 |                                                   [ 1 ]
  1791030-1970083 |                                                   [ 1 ]
  1611977-1791030 |                                                   [  ]
  1432924-1611977 |                                                   [ 1 ]
  1253871-1432924 |                                                   [ 3 ]
  1074818-1253871 |                                                   [ 4 ]
  895765-1074818  |                                                   [ 5 ]
  716712-895765   |                                                   [ 7 ]
  537659-716712   |                                                   [ 9 ]
  358606-537659   |*                                                  [ 31 ]
  179553-358606   |***                                                [ 64 ]
  500-179553      |************************************************** [ 858 ]

Storage Throughput = excellent ( 1017.47 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40545664 bp ( 40039954 non ambiguous )
   - Num Contigs Represented = 627
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:14:47 (hh:mm:ss) Elapsed Time
Round Time: 00:19:04 (hh:mm:ss) Elapsed Time : 305 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 00:00:27 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5983 repeats masked totaling 888960 bp(s).
   - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10120945 bp
       Num Contigs Represented = 233
       Non ambiguous bp:
             Initial: 10008231 bp
             After Masking: 9061416 bp
             Masked: 9.46 % 
 -- Input Database Coverage: 10120945 bp out of 79048330 bp ( 12.80 % )
Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 64620
Comparison Time: 00:07:41 (hh:mm:ss) Elapsed Time, 4299 HSPs Collected
Number of families returned by RECON: 969
Round Time: 00:09:16 (hh:mm:ss) Elapsed Time : 5 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:31 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       18799 repeats masked totaling 2837988 bp(s).
   - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30424694 bp
       Num Contigs Represented = 514
       Non ambiguous bp:
             Initial: 30031698 bp
             After Masking: 27025410 bp
             Masked: 10.01 % 
 -- Input Database Coverage: 40545639 bp out of 79048330 bp ( 51.29 % )
Sampling Time: 00:02:07 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 600060
Comparison Time: 00:41:06 (hh:mm:ss) Elapsed Time, 26657 HSPs Collected
Number of families returned by RECON: 5188
Round Time: 00:48:38 (hh:mm:ss) Elapsed Time : 17 families discovered.
   - Increasing sample size to include end piece now = 128927385


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 128927385 bp
   - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:49 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       23933 repeats masked totaling 3777503 bp(s).
   - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 38502515 bp
       Num Contigs Represented = 567
       Non ambiguous bp:
             Initial: 38088109 bp
             After Masking: 34114643 bp
             Masked: 10.43 % 
 -- Input Database Coverage: 79048154 bp out of 79048330 bp ( 100.00 % )
Sampling Time: 00:02:42 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 906531
Comparison Time: 01:00:01 (hh:mm:ss) Elapsed Time, 45654 HSPs Collected
Number of families returned by RECON: 7167
Round Time: 01:09:34 (hh:mm:ss) Elapsed Time : 36 families discovered.

RepeatScout/RECON discovery complete: 363 families found


Classification Time: 00:09:11 (hh:mm:ss) Elapsed Time


Program Time: 02:35:43 (hh:mm:ss) Elapsed Time