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.

5 tests executed, 0 fail, 0 aborted, 0 errors total.
StateNameReferenceExecutedOKWarningsErrors
H_sapiensH_sapiens5500
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 Accessiondbe9c301671e3f72d169833f77afc52d
Report timestampWed Aug 30 20:43:56 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/dbe9c301671e3f72d169833f77afc52d.yaml -mcpu -fg -fr
Benchmark Configuration
evaluation: {pos_threshold: 18}
include: [base_teaser.yaml]
meta_timestamp: 1504029140.456642
report: {name: dbe9c301671e3f72d169833f77afc52d}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    dbe9c301671e3f72d169833f77afc52d: {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 'H_sapiens.fa', title: !!python/unicode 'H_sapiens',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[20:17:51] [Main        ] framework cmd:  ./teaser.py setups_generated/dbe9c301671e3f72d169833f77afc52d.yaml -mcpu -fg -fr
[20:17:51] [Main        ] framework hash: vevev
[20:17:51] [Main        ] deployment mode: devel (True)
[20:17:51] [Main        ] Test Runner Setup - ""

[20:17:51] [Main        ] Using Teaser for data set creation
[20:17:51] [Teaser      ] Init. Creating 1 test datasets.
[20:17:51] [Teaser      ] 
[20:17:51] [Teaser      ] Creating test dbe9c301671e3f72d169833f77afc52d
[20:17:51] [Teaser      ] Failed to create test directory, probably existing
[20:17:51] [Teaser      ] remove /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/dbe9c301671e3f72d169833f77afc52d.yaml
[20:17:51] [Teaser      ] remove /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/mapping_comparison.sam
[20:17:51] [Teaser      ] remove /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/reads.fastq
[20:17:51] [Teaser      ] remove /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/reads1.fastq
[20:17:51] [Teaser      ] remove /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/reads2.fastq
[20:17:51] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d
[20:17:51] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d
[20:17:51] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[20:17:51] [Teaser      ] csample /project/teaser/genometeaser/references/H_sapiens.fa 360 0.010000
[20:17:51] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[20:17:51] [Teaser      ] Sampling as contig: 87143 regions of size 360 (pad 72), totalling 31371612 base pairs
[20:17:51] [Teaser      ] Sampling 87143 regions
[20:19:02] [Teaser      ] 10%
[20:19:10] [Teaser      ] 20%
[20:19:16] [Teaser      ] 30%
[20:19:23] [Teaser      ] 40%
[20:19:29] [Teaser      ] 50%
[20:19:36] [Teaser      ] 60%
[20:19:42] [Teaser      ] 70%
[20:19:49] [Teaser      ] 80%
[20:19:56] [Teaser      ] 90%
[20:20:03] [Teaser      ] 100%
[20:20:04] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d
[20:20:04] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 36 -N 871433  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.360.72.fasta
[20:20:04] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 36 -N 871433  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.360.72.fasta
[20:20:57] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.360.72.fasta.fastq -> ./reads.fastq
[20:20:57] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.360.72.fasta.fastq.sam -> ./mapping_comparison.sam
[20:20:57] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d
[20:20:57] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[20:20:58] [Teaser      ] Translating SAM file coordinates (as contig)...
[20:20:58] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[20:21:55] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.360.72.fasta
[20:21:55] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.360.72.fasta.index
[20:21:55] [Teaser      ] remove mapping_comparison_unfixed.sam
[20:21:55] [Teaser      ] Took 244 seconds for generating dbe9c301671e3f72d169833f77afc52d
[20:21:55] [Main        ] Data set creation completed
[20:21:55] [Main        ] 
[20:21:56] [bowtie2     ] dbe9c301671e3f72d169833f77afc52d (base: tests_base/base_mapping)
[20:21:56] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[20:21:56] [init        ] Reads: /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/reads.fastq
[20:21:56] [init        ] Output:/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/out_bowtie2.sam
[20:21:56] [map         ] Command(pre): 
[20:21:56] [map         ] Base run time file not existing, performing base run
[20:21:56] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
[20:23:10] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads.fastq -S out_bowtie2.sam
[20:23:10] [map         ]    Mapping 80.00MB to 3199.00MB with bowtie2...
[20:24:06] [map         ]    Took 55.690 (wall), 131.844 (CPU) seconds, initialization time: 34.099 (wall), 34.060 (CPU) seconds.
[20:24:06] [map         ] Command(post): 
[20:24:06] [sort_prepare] Sorting...
[20:24:27] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[20:24:58] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
748285,102702,20446,0,0,871433,4,0,0.879314255094,0.973402919877,0.923969481107

[20:24:58] [bwa         ] dbe9c301671e3f72d169833f77afc52d (base: tests_base/base_mapping)
[20:24:58] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[20:24:58] [init        ] Reads: /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/reads.fastq
[20:24:58] [init        ] Output:/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/out_bwa.sam
[20:24:58] [map         ] Command(pre): 
[20:24:58] [map         ] Base run time file not existing, performing base run
[20:24:58] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[20:27:29] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads.fastq > out_bwa.sam
[20:27:29] [map         ]    Mapping 80.00MB to 3199.00MB with bwa...
[20:31:59] [map         ]    Took 269.895 (wall), 443.080 (CPU) seconds, initialization time: 67.042 (wall), 66.796 (CPU) seconds.
[20:31:59] [map         ] Command(post): 
[20:31:59] [sort_prepare] Sorting...
[20:32:07] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[20:32:36] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
760582,103870,6981,0,0,871433,4,0,0.879842952529,0.99090498109,0.932077217428

[20:32:36] [bwamem      ] dbe9c301671e3f72d169833f77afc52d (base: tests_base/base_mapping)
[20:32:36] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[20:32:36] [init        ] Reads: /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/reads.fastq
[20:32:36] [init        ] Output:/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/out_bwamem.sam
[20:32:36] [map         ] Command(pre): 
[20:32:36] [map         ] Base run time file not existing, performing base run
[20:32:36] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -t 4 > out_bwamem.sam
[20:34:10] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq  -t 4 > out_bwamem.sam
[20:34:10] [map         ]    Mapping 80.00MB to 3199.00MB with bwamem...
[20:36:04] [map         ]    Took 113.289 (wall), 313.064 (CPU) seconds, initialization time: 44.923 (wall), 44.800 (CPU) seconds.
[20:36:04] [map         ] Command(post): 
[20:36:04] [sort_prepare] Sorting...
[20:36:12] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[20:36:40] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
717658,99987,53788,0,0,871433,2,0,0.877713433091,0.930276390052,0.903230840776

[20:36:40] [bwasw       ] dbe9c301671e3f72d169833f77afc52d (base: tests_base/base_mapping)
[20:36:40] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[20:36:40] [init        ] Reads: /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/reads.fastq
[20:36:40] [init        ] Output:/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/out_bwasw.sam
[20:36:40] [map         ] Command(pre): 
[20:36:41] [map         ] Base run time file not existing, performing base run
[20:36:41] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -t 4 > out_bwasw.sam
[20:37:53] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq  -t 4 > out_bwasw.sam
[20:37:53] [map         ]    Mapping 80.00MB to 3199.00MB with bwasw...
[20:39:17] [map         ]    Took 83.319 (wall), 215.668 (CPU) seconds, initialization time: 34.221 (wall), 34.124 (CPU) seconds.
[20:39:17] [map         ] Command(post): 
[20:39:17] [sort_prepare] Sorting...
[20:39:24] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[20:39:52] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
642780,95337,133316,0,0,871433,4,0,0.870837550144,0.82822228178,0.848995484783

[20:39:52] [ngm         ] dbe9c301671e3f72d169833f77afc52d (base: tests_base/base_mapping)
[20:39:52] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[20:39:52] [init        ] Reads: /project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/reads.fastq
[20:39:52] [init        ] Output:/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d/out_ngm.sam
[20:39:52] [map         ] Command(pre): 
[20:39:52] [map         ] Base run time file not existing, performing base run
[20:39:52] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq  --no-progress
[20:41:46] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads.fastq  --no-progress
[20:41:46] [map         ]    Mapping 80.00MB to 3199.00MB with ngm...
[20:43:19] [map         ]    Took 91.642 (wall), 202.724 (CPU) seconds, initialization time: 44.829 (wall), 52.408 (CPU) seconds.
[20:43:19] [map         ] Command(post): 
[20:43:19] [sort_prepare] Sorting...
[20:43:27] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[20:43:56] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
751658,92880,26895,0,0,871433,3,0,0.890022710642,0.965455145636,0.926205616321