RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.RQhtkJ/RM_19355.SunJul71032152024
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: 1720373534
Database = /dev/shm/rModeler.RQhtkJ/GCF_003171515.1_CUR_PTRM4_2.2   - Sequences = 41
  - Bases = 40922052
Storage Throughput = excellent ( 1037.96 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40015206 bp ( 40014566 non ambiguous )
   - Num Contigs Represented = 40
   - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:15:35 (hh:mm:ss) Elapsed Time
Round Time: 00:22:24 (hh:mm:ss) Elapsed Time : 172 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 00:00:12 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3011 repeats masked totaling 1945143 bp(s).
   - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10009515 bp
       Num Contigs Represented = 15
       Non ambiguous bp:
             Initial: 10009315 bp
             After Masking: 8026703 bp
             Masked: 19.81 % 
 -- Input Database Coverage: 10009515 bp out of 40922052 bp ( 24.46 % )
Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32640
Comparison Time: 00:04:14 (hh:mm:ss) Elapsed Time, 2524 HSPs Collected
Number of families returned by RECON: 526
Round Time: 00:06:29 (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 : 00:00:07 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       8743 repeats masked totaling 5792818 bp(s).
   - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30005656 bp
       Num Contigs Represented = 36
       Non ambiguous bp:
             Initial: 30005216 bp
             After Masking: 24116718 bp
             Masked: 19.62 % 
 -- Input Database Coverage: 40015171 bp out of 40922052 bp ( 97.78 % )
Sampling Time: 00:01:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 290703
Comparison Time: 00:22:37 (hh:mm:ss) Elapsed Time, 19555 HSPs Collected
Number of families returned by RECON: 2175
Round Time: 00:30:28 (hh:mm:ss) Elapsed Time : 22 families discovered.
   - Increasing sample size to include end piece now = 90912537


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 90912537 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       373 repeats masked totaling 230620 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 906662 bp
       Num Contigs Represented = 7
       Non ambiguous bp:
             Initial: 906662 bp
             After Masking: 674236 bp
             Masked: 25.64 % 
 -- Input Database Coverage: 40921833 bp out of 40922052 bp ( 100.00 % )
Sampling Time: 00:00:05 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 253
Comparison Time: 00:00:15 (hh:mm:ss) Elapsed Time, 7 HSPs Collected
Round Time: 00:00:20 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 199 families found


Classification Time: 00:22:27 (hh:mm:ss) Elapsed Time


Program Time: 01:22:08 (hh:mm:ss) Elapsed Time