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
D_melanogasterD_melanogaster5500
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 Accession75a17aa3ae45687f5c9f13afd04e2aae
Report timestampWed May 17 23:42:28 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/75a17aa3ae45687f5c9f13afd04e2aae.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 75}
include: [base_teaser.yaml]
meta_timestamp: 1495056778.165969
report: {name: 75a17aa3ae45687f5c9f13afd04e2aae}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    75a17aa3ae45687f5c9f13afd04e2aae: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 100,
      insert_size_error: 50, mutation_indel_avg_len: 1.0, mutation_indel_frac: 0.3,
      mutation_rate: 0.01, paired: true, platform: !!python/unicode 'illumina', read_length: 150,
      reference: !!python/unicode 'D_melanogaster.fasta', title: !!python/unicode 'D_melanogaster',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[23:33:04] [Main        ] framework cmd:  ./teaser.py setups_generated/75a17aa3ae45687f5c9f13afd04e2aae.yaml -mcpu
[23:33:04] [Main        ] framework hash: vevev
[23:33:04] [Main        ] deployment mode: devel (True)
[23:33:04] [Main        ] Test Runner Setup - ""

[23:33:04] [Main        ] Using Teaser for data set creation
[23:33:04] [Teaser      ] Init. Creating 1 test datasets.
[23:33:04] [Teaser      ] 
[23:33:04] [Teaser      ] Creating test 75a17aa3ae45687f5c9f13afd04e2aae
[23:33:04] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae
[23:33:04] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae
[23:33:04] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[23:33:04] [Teaser      ] csample /project/teaser/genometeaser/references/D_melanogaster.fasta 1500 0.250000
[23:33:04] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[23:33:04] [Teaser      ] Sampling as contig: 23954 regions of size 1500 (pad 300), totalling 35931498 base pairs
[23:33:04] [Teaser      ] Sampling 23954 regions
[23:33:06] [Teaser      ] 10%
[23:33:08] [Teaser      ] 20%
[23:33:09] [Teaser      ] 30%
[23:33:11] [Teaser      ] 40%
[23:33:13] [Teaser      ] 50%
[23:33:15] [Teaser      ] 60%
[23:33:17] [Teaser      ] 70%
[23:33:19] [Teaser      ] 80%
[23:33:21] [Teaser      ] 90%
[23:33:22] [Teaser      ] 100%
[23:33:23] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae
[23:33:23] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 119771 --mp  --ll 100 --le 50  --hi 0.003000  --hs 0.007000  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1500.300.fasta
[23:33:23] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 119771 --mp  --ll 100 --le 50  --hi 0.003000  --hs 0.007000  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1500.300.fasta
[23:34:57] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1500.300.fasta_1.fastq -> ./reads1.fastq
[23:34:57] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1500.300.fasta_2.fastq -> ./reads2.fastq
[23:34:57] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1500.300.fasta.fastq.sam -> ./mapping_comparison.sam
[23:34:57] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae
[23:34:57] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[23:34:57] [Teaser      ] Translating SAM file coordinates (as contig)...
[23:34:57] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[23:35:17] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1500.300.fasta
[23:35:17] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1500.300.fasta.index
[23:35:17] [Teaser      ] remove mapping_comparison_unfixed.sam
[23:35:17] [Teaser      ] Took 133 seconds for generating 75a17aa3ae45687f5c9f13afd04e2aae
[23:35:17] [Main        ] Data set creation completed
[23:35:17] [Main        ] 
[23:35:18] [bowtie2     ] 75a17aa3ae45687f5c9f13afd04e2aae (base: tests_base/base_mapping)
[23:35:18] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[23:35:18] [init        ] Reads: /project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae/reads1.fastq
[23:35:18] [init        ] Output:/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae/out_bowtie2.sam
[23:35:18] [map         ] Command(pre): 
[23:35:18] [map         ] Base run time file not existing, performing base run
[23:35:18] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
[23:35:20] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
[23:35:20] [map         ]    Mapping 76.00MB to 146.00MB with bowtie2...
[23:36:04] [map         ]    Took 43.778 (wall), 171.504 (CPU) seconds, initialization time: 0.274 (wall), 0.254 (CPU) seconds.
[23:36:04] [map         ] Command(post): 
[23:36:04] [sort_prepare] Sorting...
[23:36:13] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[23:36:27] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
218228,21225,89,0,0,239542,0,0,0.911360475751,0.999592335915,0.953439500186

[23:36:27] [bwa         ] 75a17aa3ae45687f5c9f13afd04e2aae (base: tests_base/base_mapping)
[23:36:27] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[23:36:27] [init        ] Reads: /project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae/reads1.fastq
[23:36:27] [init        ] Output:/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae/out_bwa.sam
[23:36:27] [map         ] Command(pre): 
[23:36:27] [map         ] Base run time file not existing, performing base run
[23:36:27] [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
[23:36:29] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq  -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads2.fastq  -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
[23:36:29] [map         ]    Mapping 76.00MB to 146.00MB with bwa...
[23:37:26] [map         ]    Took 56.383 (wall), 146.190 (CPU) seconds, initialization time: 0.262 (wall), 0.205 (CPU) seconds.
[23:37:26] [map         ] Command(post): 
[23:37:26] [sort_prepare] Sorting...
[23:37:29] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[23:37:42] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
186174,17603,35765,0,0,239542,0,0,0.913616355133,0.838852117023,0.874639430982

[23:37:42] [bwamem      ] 75a17aa3ae45687f5c9f13afd04e2aae (base: tests_base/base_mapping)
[23:37:42] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[23:37:42] [init        ] Reads: /project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae/reads1.fastq
[23:37:42] [init        ] Output:/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae/out_bwamem.sam
[23:37:42] [map         ] Command(pre): 
[23:37:42] [map         ] Base run time file not existing, performing base run
[23:37:42] [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
[23:37:44] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq  -t 4 > out_bwamem.sam
[23:37:44] [map         ]    Mapping 76.00MB to 146.00MB with bwamem...
[23:38:19] [map         ]    Took 34.822 (wall), 99.897 (CPU) seconds, initialization time: 0.318 (wall), 0.176 (CPU) seconds.
[23:38:19] [map         ] Command(post): 
[23:38:19] [sort_prepare] Sorting...
[23:38:22] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[23:38:33] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
221440,18102,0,0,0,239542,0,0,0.924430788755,1.0,0.960731655466

[23:38:33] [bwasw       ] 75a17aa3ae45687f5c9f13afd04e2aae (base: tests_base/base_mapping)
[23:38:33] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[23:38:33] [init        ] Reads: /project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae/reads1.fastq
[23:38:33] [init        ] Output:/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae/out_bwasw.sam
[23:38:33] [map         ] Command(pre): 
[23:38:33] [map         ] Base run time file not existing, performing base run
[23:38:33] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq  -t 4 > out_bwasw.sam
[23:38:36] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq  -t 4 > out_bwasw.sam
[23:38:36] [map         ]    Mapping 76.00MB to 146.00MB with bwasw...
[23:41:30] [map         ]    Took 173.253 (wall), 330.980 (CPU) seconds, initialization time: 0.208 (wall), 0.171 (CPU) seconds.
[23:41:30] [map         ] Command(post): 
[23:41:30] [sort_prepare] Sorting...
[23:41:33] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[23:41:53] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
218882,20656,1,3,27,239542,0,0,0.913767335454,0.999995431349,0.954938800797

[23:41:53] [ngm         ] 75a17aa3ae45687f5c9f13afd04e2aae (base: tests_base/base_mapping)
[23:41:53] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[23:41:53] [init        ] Reads: /project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae/reads1.fastq
[23:41:53] [init        ] Output:/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae/out_ngm.sam
[23:41:53] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/D_melanogaster.fasta 
[23:41:54] [map         ] Base run time file not existing, performing base run
[23:41:55] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads_base.fastq  --no-progress
[23:42:00] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4  --no-progress
[23:42:00] [map         ]    Mapping 76.00MB to 146.00MB with ngm...
[23:42:16] [map         ]    Took 15.373 (wall), 40.336 (CPU) seconds, initialization time: 2.766 (wall), 2.836 (CPU) seconds.
[23:42:16] [map         ] Command(post): 
[23:42:16] [sort_prepare] Sorting...
[23:42:18] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[23:42:28] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
220083,19436,23,0,0,239542,0,0,0.918854036632,0.999895504893,0.957663312483