RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.2ei0iA/RM_22341.MonAug121753072024
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: 1723510386
Database = /dev/shm/rModeler.2ei0iA/GCA_000855695.1_Cryp_gatt_CA1873_V1   - Sequences = 33
  - Bases = 17438253
Storage Throughput = excellent ( 1049.11 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 17438128 bp ( 17389784 non ambiguous )
   - Num Contigs Represented = 33
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:04:18 (hh:mm:ss) Elapsed Time
Round Time: 00:04:46 (hh:mm:ss) Elapsed Time : 16 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:01 (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...
       363 repeats masked totaling 91039 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10050131 bp
       Num Contigs Represented = 30
       Non ambiguous bp:
             Initial: 10012805 bp
             After Masking: 9911564 bp
             Masked: 1.01 % 
 -- Input Database Coverage: 10050131 bp out of 17438253 bp ( 57.63 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33670
Comparison Time: 00:04:47 (hh:mm:ss) Elapsed Time, 1505 HSPs Collected
Number of families returned by RECON: 561
Round Time: 00:05:10 (hh:mm:ss) Elapsed Time : 1 families discovered.
   - Increasing sample size to include end piece now = 37438253


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 37438253 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       273 repeats masked totaling 54805 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 7387917 bp
       Num Contigs Represented = 30
       Non ambiguous bp:
             Initial: 7376899 bp
             After Masking: 7313611 bp
             Masked: 0.86 % 
 -- Input Database Coverage: 17438048 bp out of 17438253 bp ( 100.00 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 18721
Comparison Time: 00:02:59 (hh:mm:ss) Elapsed Time, 823 HSPs Collected
Number of families returned by RECON: 357
Round Time: 00:03:13 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 17 families found


Classification Time: 00:00:32 (hh:mm:ss) Elapsed Time


Program Time: 00:13:41 (hh:mm:ss) Elapsed Time