Tests Overview

Use the links in the list below to view results for an individual data set, or navigate this page to compare mapper performance across all data sets.

2 tests executed, 0 fail, 0 aborted, 0 errors total.
StateNameReferenceExecutedOKWarningsErrors
D_melanogasterD_melanogaster2200
Errors and Warnings
No problems were encountered.
Results: Correctly Mapped Reads
Results: Correct/s
Results: Precision
Results: Recall
Results: F-Measure
Raw Results
Setup

This section contains information about the benchmarking process itself and can be shared in order to reproduce results and diagnose problems.

Teaser Accession47ed064b8a7255de5257058de7620d9c
Report timestampTue Sep 12 17:14:15 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/47ed064b8a7255de5257058de7620d9c.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 18}
include: [base_teaser.yaml]
meta_timestamp: 1505228222.220823
report: {name: 47ed064b8a7255de5257058de7620d9c}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    47ed064b8a7255de5257058de7620d9c: {coverage: 1.0, error_rate_mult: 1.0, mutation_indel_avg_len: 1.0,
      mutation_indel_frac: 0.3, mutation_rate: 0.001, paired: false, platform: !!python/unicode 'illumina',
      read_length: 36, reference: !!python/unicode 'D_melanogaster.fasta', title: !!python/unicode 'D_melanogaster',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bwa, bwamem]
test_parameters: []
threads: 4
Log
[16:57:20] [Main        ] framework cmd:  ./teaser.py setups_generated/47ed064b8a7255de5257058de7620d9c.yaml -mcpu
[16:57:20] [Main        ] framework hash: vevev
[16:57:20] [Main        ] deployment mode: devel (True)
[16:57:20] [Main        ] Test Runner Setup - ""

[16:57:20] [Main        ] Using Teaser for data set creation
[16:57:21] [Teaser      ] Init. Creating 1 test datasets.
[16:57:21] [Teaser      ] 
[16:57:21] [Teaser      ] Creating test 47ed064b8a7255de5257058de7620d9c
[16:57:21] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c
[16:57:21] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c
[16:57:21] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[16:57:21] [Teaser      ] csample /project/teaser/genometeaser/references/D_melanogaster.fasta 360 0.250000
[16:57:21] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[16:57:21] [Teaser      ] Sampling as contig: 99809 regions of size 360 (pad 72), totalling 35931498 base pairs
[16:57:21] [Teaser      ] Sampling 99809 regions
[16:58:07] [Teaser      ] 10%
[16:58:18] [Teaser      ] 20%
[16:58:28] [Teaser      ] 30%
[16:58:38] [Teaser      ] 40%
[16:58:48] [Teaser      ] 50%
[16:58:58] [Teaser      ] 60%
[16:59:09] [Teaser      ] 70%
[16:59:19] [Teaser      ] 80%
[16:59:30] [Teaser      ] 90%
[16:59:40] [Teaser      ] 100%
[16:59:55] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c
[16:59:56] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 36 -N 998097  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.360.72.fasta
[16:59:56] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 36 -N 998097  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.360.72.fasta
[17:02:30] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.360.72.fasta.fastq -> ./reads.fastq
[17:02:30] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.360.72.fasta.fastq.sam -> ./mapping_comparison.sam
[17:02:30] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c
[17:02:30] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[17:02:30] [Teaser      ] Translating SAM file coordinates (as contig)...
[17:02:30] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[17:05:15] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.360.72.fasta
[17:05:15] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.360.72.fasta.index
[17:05:15] [Teaser      ] remove mapping_comparison_unfixed.sam
[17:05:15] [Teaser      ] Took 474 seconds for generating 47ed064b8a7255de5257058de7620d9c
[17:05:15] [Main        ] Data set creation completed
[17:05:15] [Main        ] 
[17:05:16] [bwa         ] 47ed064b8a7255de5257058de7620d9c (base: tests_base/base_mapping)
[17:05:16] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[17:05:16] [init        ] Reads: /project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c/reads.fastq
[17:05:16] [init        ] Output:/project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c/out_bwa.sam
[17:05:16] [map         ] Command(pre): 
[17:05:16] [map         ] Base run time file not existing, performing base run
[17:05:16] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[17:05:54] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
[17:05:54] [map         ]    Mapping 91.00MB to 146.00MB with bwa...
[17:07:34] [map         ]    Took 99.037 (wall), 135.196 (CPU) seconds, initialization time: 3.348 (wall), 2.960 (CPU) seconds.
[17:07:34] [map         ] Command(post): 
[17:07:35] [sort_prepare] Sorting...
[17:09:22] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[17:10:46] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
855231,134306,8560,0,0,998097,1,0,0.864273897793,0.990090195429,0.922913806946

[17:10:46] [bwamem      ] 47ed064b8a7255de5257058de7620d9c (base: tests_base/base_mapping)
[17:10:46] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[17:10:46] [init        ] Reads: /project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c/reads.fastq
[17:10:46] [init        ] Output:/project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c/out_bwamem.sam
[17:10:46] [map         ] Command(pre): 
[17:10:46] [map         ] Base run time file not existing, performing base run
[17:10:46] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq  -t 4 > out_bwamem.sam
[17:11:04] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwamem.sam
[17:11:05] [map         ]    Mapping 91.00MB to 146.00MB with bwamem...
[17:12:04] [map         ]    Took 57.227 (wall), 117.984 (CPU) seconds, initialization time: 7.255 (wall), 3.276 (CPU) seconds.
[17:12:04] [map         ] Command(post): 
[17:12:12] [sort_prepare] Sorting...
[17:12:49] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[17:14:14] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
806537,126740,64820,0,0,998097,1,0,0.864198946294,0.92561028373,0.893851052346