RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.R4qiNs/RM_10327.FriSep201642472024
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: 1726875766
Database = /dev/shm/rModeler.R4qiNs/GCA_000387425.2_pir_scaffolds_v1   - Sequences = 5887
  - Bases = 42968084
  - N50 = 23284
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  163554-175201 |                                                   [ 2 ]
  151907-163553 |                                                   [ 1 ]
  140260-151906 |                                                   [  ]
  128614-140260 |                                                   [ 1 ]
  116967-128613 |                                                   [ 1 ]
  105320-116966 |                                                   [ 3 ]
  93673-105319  |                                                   [ 7 ]
  82027-93673   |                                                   [ 11 ]
  70380-82026   |                                                   [ 18 ]
  58733-70379   |                                                   [ 31 ]
  47086-58732   |                                                   [ 85 ]
  35440-47086   |*                                                  [ 111 ]
  23793-35439   |**                                                 [ 206 ]
  12146-23792   |*****                                              [ 496 ]
  500-12146     |************************************************** [ 4914 ]

Storage Throughput = excellent ( 1087.01 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40280087 bp ( 40008687 non ambiguous )
   - Num Contigs Represented = 5513
   - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:20:49 (hh:mm:ss) Elapsed Time
Round Time: 00:22:46 (hh:mm:ss) Elapsed Time : 201 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       1953 repeats masked totaling 368016 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10064480 bp
       Num Contigs Represented = 1410
       Non ambiguous bp:
             Initial: 10000153 bp
             After Masking: 9624214 bp
             Masked: 3.76 % 
 -- Input Database Coverage: 10064480 bp out of 42968084 bp ( 23.42 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 1021735
Comparison Time: 00:08:42 (hh:mm:ss) Elapsed Time, 4404 HSPs Collected
Number of families returned by RECON: 1605
Round Time: 00:09:20 (hh:mm:ss) Elapsed Time : 1 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 00:00:35 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5768 repeats masked totaling 1096201 bp(s).
   - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30215543 bp
       Num Contigs Represented = 4187
       Non ambiguous bp:
             Initial: 30008470 bp
             After Masking: 28881135 bp
             Masked: 3.76 % 
 -- Input Database Coverage: 40280023 bp out of 42968084 bp ( 93.74 % )
Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 9281586
Comparison Time: 00:43:29 (hh:mm:ss) Elapsed Time, 37655 HSPs Collected
Number of families returned by RECON: 7671
Round Time: 00:46:42 (hh:mm:ss) Elapsed Time : 40 families discovered.
   - Increasing sample size to include end piece now = 92903604


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 92903604 bp
   - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       601 repeats masked totaling 126417 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 2687929 bp
       Num Contigs Represented = 401
       Non ambiguous bp:
             Initial: 2667864 bp
             After Masking: 2540315 bp
             Masked: 4.78 % 
 -- Input Database Coverage: 42967952 bp out of 42968084 bp ( 100.00 % )
Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 80601
Comparison Time: 00:01:51 (hh:mm:ss) Elapsed Time, 250 HSPs Collected
Number of families returned by RECON: 161
Round Time: 00:02:00 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 242 families found


Classification Time: 00:04:59 (hh:mm:ss) Elapsed Time


Program Time: 01:25:47 (hh:mm:ss) Elapsed Time