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
Schizosaccharomyces_pombeSchizosaccharomyces_pombe5500
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 Accession78245a202e759eede079b41dad2c7157
Report timestampWed May 17 23:36:20 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/78245a202e759eede079b41dad2c7157.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 50}
include: [base_teaser.yaml]
meta_timestamp: 1495056502.872635
report: {name: 78245a202e759eede079b41dad2c7157}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    78245a202e759eede079b41dad2c7157: {coverage: 1.0, error_rate_mult: 1.0, mutation_indel_avg_len: 1.0,
      mutation_indel_frac: 0.3, mutation_rate: 0.01, paired: false, platform: !!python/unicode 'illumina',
      read_length: 100, reference: !!python/unicode 'Schizosaccharomyces_pombe.fa',
      title: !!python/unicode 'Schizosaccharomyces_pombe', type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[23:32:36] [Main        ] framework cmd:  ./teaser.py setups_generated/78245a202e759eede079b41dad2c7157.yaml -mcpu
[23:32:36] [Main        ] framework hash: vevev
[23:32:36] [Main        ] deployment mode: devel (True)
[23:32:36] [Main        ] Test Runner Setup - ""

[23:32:36] [Main        ] Using Teaser for data set creation
[23:32:37] [Teaser      ] Init. Creating 1 test datasets.
[23:32:37] [Teaser      ] 
[23:32:37] [Teaser      ] Creating test 78245a202e759eede079b41dad2c7157
[23:32:37] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157
[23:32:37] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157
[23:32:37] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa.teaser.findex
[23:32:37] [Teaser      ] csample /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa 1000 0.500000
[23:32:37] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa.teaser.findex
[23:32:37] [Teaser      ] Sampling as contig: 6315 regions of size 1000 (pad 200), totalling 6315689 base pairs
[23:32:37] [Teaser      ] Sampling 6315 regions
[23:32:39] [Teaser      ] 10%
[23:32:40] [Teaser      ] 20%
[23:32:41] [Teaser      ] 30%
[23:32:42] [Teaser      ] 40%
[23:32:44] [Teaser      ] 50%
[23:32:45] [Teaser      ] 60%
[23:32:46] [Teaser      ] 70%
[23:32:48] [Teaser      ] 80%
[23:32:50] [Teaser      ] 90%
[23:32:53] [Teaser      ] 100%
[23:32:53] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157
[23:32:53] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 100 -N 150000  --ll 500 --le 50  --hi 0.003000  --hs 0.007000  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa.sampled.2.1000.200.fasta
[23:32:53] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 100 -N 150000  --ll 500 --le 50  --hi 0.003000  --hs 0.007000  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa.sampled.2.1000.200.fasta
[23:33:22] [Teaser      ] move /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa.sampled.2.1000.200.fasta.fastq -> ./reads.fastq
[23:33:22] [Teaser      ] move /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa.sampled.2.1000.200.fasta.fastq.sam -> ./mapping_comparison.sam
[23:33:22] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157
[23:33:22] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[23:33:22] [Teaser      ] Translating SAM file coordinates (as contig)...
[23:33:22] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa.teaser.findex
[23:33:37] [Teaser      ] remove /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa.sampled.2.1000.200.fasta
[23:33:37] [Teaser      ] remove /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa.sampled.2.1000.200.fasta.index
[23:33:37] [Teaser      ] remove mapping_comparison_unfixed.sam
[23:33:37] [Teaser      ] Took 60 seconds for generating 78245a202e759eede079b41dad2c7157
[23:33:37] [Main        ] Data set creation completed
[23:33:37] [Main        ] 
[23:33:37] [bowtie2     ] 78245a202e759eede079b41dad2c7157 (base: tests_base/base_mapping)
[23:33:37] [init        ] Ref:   /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa
[23:33:37] [init        ] Reads: /project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157/reads.fastq
[23:33:37] [init        ] Output:/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157/out_bowtie2.sam
[23:33:37] [map         ] Command(pre): 
[23:33:37] [map         ] Base run time file not existing, performing base run
[23:33:37] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa_bt -U reads_base.fastq -S out_bowtie2.sam
[23:33:40] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa_bt -U reads.fastq -S out_bowtie2.sam
[23:33:40] [map         ]    Mapping 33.00MB to 12.00MB with bowtie2...
[23:33:46] [map         ]    Took 5.741 (wall), 20.434 (CPU) seconds, initialization time: 0.243 (wall), 0.195 (CPU) seconds.
[23:33:46] [map         ] Command(post): 
[23:33:46] [sort_prepare] Sorting...
[23:33:48] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[23:33:54] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
145973,3757,270,0,0,150000,0,0,0.974908168036,0.998153757787,0.986394029185

[23:33:54] [bwa         ] 78245a202e759eede079b41dad2c7157 (base: tests_base/base_mapping)
[23:33:54] [init        ] Ref:   /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa
[23:33:54] [init        ] Reads: /project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157/reads.fastq
[23:33:54] [init        ] Output:/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157/out_bwa.sam
[23:33:54] [map         ] Command(pre): 
[23:33:55] [map         ] Base run time file not existing, performing base run
[23:33:55] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[23:33:57] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa out_bwa.sam.bwa reads.fastq > out_bwa.sam
[23:33:57] [map         ]    Mapping 33.00MB to 12.00MB with bwa...
[23:34:42] [map         ]    Took 44.493 (wall), 40.901 (CPU) seconds, initialization time: 0.099 (wall), 0.029 (CPU) seconds.
[23:34:42] [map         ] Command(post): 
[23:34:42] [sort_prepare] Sorting...
[23:34:43] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[23:34:49] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
133523,3399,13078,0,0,150000,0,0,0.975175647449,0.910791877272,0.941884785361

[23:34:49] [bwamem      ] 78245a202e759eede079b41dad2c7157 (base: tests_base/base_mapping)
[23:34:49] [init        ] Ref:   /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa
[23:34:49] [init        ] Reads: /project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157/reads.fastq
[23:34:49] [init        ] Output:/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157/out_bwamem.sam
[23:34:49] [map         ] Command(pre): 
[23:34:49] [map         ] Base run time file not existing, performing base run
[23:34:49] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq  -t 4 > out_bwamem.sam
[23:34:51] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq  -t 4 > out_bwamem.sam
[23:34:51] [map         ]    Mapping 33.00MB to 12.00MB with bwamem...
[23:34:59] [map         ]    Took 7.785 (wall), 14.823 (CPU) seconds, initialization time: 0.233 (wall), 0.019 (CPU) seconds.
[23:34:59] [map         ] Command(post): 
[23:34:59] [sort_prepare] Sorting...
[23:35:00] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[23:35:11] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
146227,3771,2,0,0,150000,0,0,0.974859664796,0.999986322822,0.987263146168

[23:35:11] [bwasw       ] 78245a202e759eede079b41dad2c7157 (base: tests_base/base_mapping)
[23:35:11] [init        ] Ref:   /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa
[23:35:11] [init        ] Reads: /project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157/reads.fastq
[23:35:11] [init        ] Output:/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157/out_bwasw.sam
[23:35:11] [map         ] Command(pre): 
[23:35:11] [map         ] Base run time file not existing, performing base run
[23:35:11] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq  -t 4 > out_bwasw.sam
[23:35:13] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq  -t 4 > out_bwasw.sam
[23:35:13] [map         ]    Mapping 33.00MB to 12.00MB with bwasw...
[23:35:35] [map         ]    Took 21.714 (wall), 76.362 (CPU) seconds, initialization time: 0.055 (wall), 0.021 (CPU) seconds.
[23:35:35] [map         ] Command(post): 
[23:35:35] [sort_prepare] Sorting...
[23:35:36] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[23:35:42] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
145775,3755,470,0,5,150000,0,0,0.974887982345,0.996786214913,0.985715493196

[23:35:42] [ngm         ] 78245a202e759eede079b41dad2c7157 (base: tests_base/base_mapping)
[23:35:42] [init        ] Ref:   /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa
[23:35:42] [init        ] Reads: /project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157/reads.fastq
[23:35:42] [init        ] Output:/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157/out_ngm.sam
[23:35:42] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa 
[23:35:58] [map         ] Base run time file not existing, performing base run
[23:35:58] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa -t 4 --qry reads_base.fastq  --no-progress
[23:36:04] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa -t 4 --qry reads.fastq  --no-progress
[23:36:04] [map         ]    Mapping 33.00MB to 12.00MB with ngm...
[23:36:11] [map         ]    Took 6.771 (wall), 14.842 (CPU) seconds, initialization time: 2.581 (wall), 3.024 (CPU) seconds.
[23:36:11] [map         ] Command(post): 
[23:36:11] [sort_prepare] Sorting...
[23:36:14] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[23:36:20] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
146204,3796,0,0,0,150000,0,0,0.974693333333,1.0,0.987184507974