RepeatModeler Version 2.0.4
===========================
Using output directory = /data/tmp/rModeler.uMy7Af/RM_3028970.WedApr160520502025
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: 1744806047
Database = /data/tmp/rModeler.uMy7Af/GCA_023637945.2_bPhaSup1.pri   - Sequences = 65
  - Bases = 1020009783
Storage Throughput = excellent ( 1563.58 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40257438 bp ( 40039248 non ambiguous )
   - Num Contigs Represented = 37
   - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:11:33 (hh:mm:ss) Elapsed Time
Round Time: 00:13:33 (hh:mm:ss) Elapsed Time : 82 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2504 repeats masked totaling 596153 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10129251 bp
       Num Contigs Represented = 31
       Non ambiguous bp:
             Initial: 10031688 bp
             After Masking: 9336009 bp
             Masked: 6.93 % 
 -- Input Database Coverage: 10129251 bp out of 1020009783 bp ( 0.99 % )
Sampling Time: 00:00:37 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 31878
Comparison Time: 00:05:29 (hh:mm:ss) Elapsed Time, 441 HSPs Collected
Number of families returned by RECON: 272
Round Time: 00:06:06 (hh:mm:ss) Elapsed Time : 0 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       7693 repeats masked totaling 1860155 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30128156 bp
       Num Contigs Represented = 34
       Non ambiguous bp:
             Initial: 30007529 bp
             After Masking: 27874625 bp
             Masked: 7.11 % 
 -- Input Database Coverage: 40257407 bp out of 1020009783 bp ( 3.95 % )
Sampling Time: 00:01:40 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 284635
Comparison Time: 00:30:30 (hh:mm:ss) Elapsed Time, 4411 HSPs Collected
Number of families returned by RECON: 1858
Round Time: 00:32:24 (hh:mm:ss) Elapsed Time : 7 families discovered.


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 90000000 bp
   - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:02:32 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       22192 repeats masked totaling 5365571 bp(s).
   - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 90467438 bp
       Num Contigs Represented = 38
       Non ambiguous bp:
             Initial: 90027267 bp
             After Masking: 83974203 bp
             Masked: 6.72 % 
 -- Input Database Coverage: 130724845 bp out of 1020009783 bp ( 12.82 % )
Sampling Time: 00:05:04 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2566245
Comparison Time: 02:45:05 (hh:mm:ss) Elapsed Time, 37690 HSPs Collected
Number of families returned by RECON: 12102
Round Time: 02:51:26 (hh:mm:ss) Elapsed Time : 51 families discovered.


RepeatModeler Round # 5
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 270000000 bp
   - Sequence extraction : 00:06:12 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:08:05 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       75924 repeats masked totaling 18153327 bp(s).
   - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 271008601 bp
       Num Contigs Represented = 44
       Non ambiguous bp:
             Initial: 270001289 bp
             After Masking: 249564962 bp
             Masked: 7.57 % 
 -- Input Database Coverage: 401733446 bp out of 1020009783 bp ( 39.39 % )
Sampling Time: 00:15:36 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 23001153
Comparison Time: 21:24:03 (hh:mm:ss) Elapsed Time, 194058 HSPs Collected
Number of families returned by RECON: 80353
Round Time: 22:07:47 (hh:mm:ss) Elapsed Time : 143 families discovered.

RepeatScout/RECON discovery complete: 283 families found


Classification Time: 00:08:42 (hh:mm:ss) Elapsed Time


Program Time: 25:59:58 (hh:mm:ss) Elapsed Time