RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.qDCaaA/RM_25316.MonAug122010502024
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: 1723518649
Database = /dev/shm/rModeler.qDCaaA/GCA_001599035.1_JCM_9410_assembly_v001   - Sequences = 23
  - Bases = 37316984
Storage Throughput = excellent ( 1044.03 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 37316879 bp ( 36954135 non ambiguous )
   - Num Contigs Represented = 23
   - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:15:27 (hh:mm:ss) Elapsed Time
Round Time: 00:16:41 (hh:mm:ss) Elapsed Time : 21 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       262 repeats masked totaling 30372 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10100218 bp
       Num Contigs Represented = 12
       Non ambiguous bp:
             Initial: 10039732 bp
             After Masking: 9972316 bp
             Masked: 0.67 % 
 -- Input Database Coverage: 10100218 bp out of 37316984 bp ( 27.07 % )
Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33153
Comparison Time: 00:17:38 (hh:mm:ss) Elapsed Time, 1522 HSPs Collected
Number of families returned by RECON: 574
Round Time: 00:25:19 (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 : 00:00:07 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       717 repeats masked totaling 84009 bp(s).
   - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 27216587 bp
       Num Contigs Represented = 20
       Non ambiguous bp:
             Initial: 26914329 bp
             After Masking: 26734330 bp
             Masked: 0.67 % 
 -- Input Database Coverage: 37316805 bp out of 37316984 bp ( 100.00 % )
Sampling Time: 00:01:30 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 241165
Comparison Time: 01:12:52 (hh:mm:ss) Elapsed Time, 12082 HSPs Collected
Number of families returned by RECON: 2728
Round Time: 06:33:03 (hh:mm:ss) Elapsed Time : 7 families discovered.

RepeatScout/RECON discovery complete: 28 families found


Classification Time: 00:03:16 (hh:mm:ss) Elapsed Time


Program Time: 07:18:19 (hh:mm:ss) Elapsed Time