RepeatModeler Version 2.0.4
===========================
Using output directory = /scratch/tmp/rModeler.ZA2j4W/RM_1433921.MonNov180822532024
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: 1731946972
Database = /scratch/tmp/rModeler.ZA2j4W/GCA_023333525.1_rAspTig1.0.p   - Sequences = 74
  - Bases = 1335668279
Storage Throughput = excellent ( 1539.60 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40007014 bp ( 40007014 non ambiguous )
   - Num Contigs Represented = 39
   - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:07:45 (hh:mm:ss) Elapsed Time
Round Time: 00:11:43 (hh:mm:ss) Elapsed Time : 629 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       18250 repeats masked totaling 3299884 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10002044 bp
       Num Contigs Represented = 33
       Non ambiguous bp:
             Initial: 10002044 bp
             After Masking: 6220064 bp
             Masked: 37.81 % 
 -- Input Database Coverage: 10002044 bp out of 1335668279 bp ( 0.75 % )
Sampling Time: 00:00:58 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31125
Comparison Time: 00:02:54 (hh:mm:ss) Elapsed Time, 13749 HSPs Collected
Number of families returned by RECON: 1501
Round Time: 00:04:09 (hh:mm:ss) Elapsed Time : 32 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       59165 repeats masked totaling 10787569 bp(s).
   - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30004966 bp
       Num Contigs Represented = 38
       Non ambiguous bp:
             Initial: 30004966 bp
             After Masking: 17921170 bp
             Masked: 40.27 % 
 -- Input Database Coverage: 40007010 bp out of 1335668279 bp ( 3.00 % )
Sampling Time: 00:02:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 283128
Comparison Time: 00:12:10 (hh:mm:ss) Elapsed Time, 49058 HSPs Collected
Number of families returned by RECON: 4450
Round Time: 00:15:19 (hh:mm:ss) Elapsed Time : 100 families discovered.


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 90000000 bp
   - Sequence extraction : 00:02:39 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:03:35 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       191067 repeats masked totaling 34412096 bp(s).
   - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 90021358 bp
       Num Contigs Represented = 44
       Non ambiguous bp:
             Initial: 90021258 bp
             After Masking: 51719442 bp
             Masked: 42.55 % 
 -- Input Database Coverage: 130028368 bp out of 1335668279 bp ( 9.74 % )
Sampling Time: 00:06:57 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2539131
Comparison Time: 01:02:09 (hh:mm:ss) Elapsed Time, 218250 HSPs Collected
Number of families returned by RECON: 13102
Round Time: 01:13:36 (hh:mm:ss) Elapsed Time : 438 families discovered.


RepeatModeler Round # 5
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 270000000 bp
   - Sequence extraction : 00:07:57 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:11:56 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       642515 repeats masked totaling 116081522 bp(s).
   - TE Masking time 00:03:01 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 270032616 bp
       Num Contigs Represented = 54
       Non ambiguous bp:
             Initial: 270031416 bp
             After Masking: 142634597 bp
             Masked: 47.18 % 
 -- Input Database Coverage: 400060984 bp out of 1335668279 bp ( 29.95 % )
Sampling Time: 00:23:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 22845420
Comparison Time: 06:57:54 (hh:mm:ss) Elapsed Time, 486248 HSPs Collected
Number of families returned by RECON: 41694
Round Time: 07:44:17 (hh:mm:ss) Elapsed Time : 995 families discovered.

RepeatScout/RECON discovery complete: 2194 families found


Classification Time: 00:31:20 (hh:mm:ss) Elapsed Time


Program Time: 10:00:24 (hh:mm:ss) Elapsed Time