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
Saccharomyces_cerevisiaeSaccharomyces_cerevisiae5500
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 Accessionde78d5f7fdafaffb89a6272863840c5f
Report timestampWed Oct 3 16:41:15 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/de78d5f7fdafaffb89a6272863840c5f.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 75}
include: [base_teaser.yaml]
meta_timestamp: 1538577210.183901
report: {name: de78d5f7fdafaffb89a6272863840c5f}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    de78d5f7fdafaffb89a6272863840c5f: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 400,
      insert_size_error: 50, mutation_indel_avg_len: 1.0, mutation_indel_frac: 0.3,
      mutation_rate: 0.02, paired: true, platform: !!python/unicode 'illumina', read_length: 150,
      reference: !!python/unicode 'Saccharomyces_cerevisiae.fasta', title: !!python/unicode 'Saccharomyces_cerevisiae',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[16:33:31] [Main        ] framework cmd:  ./teaser.py setups_generated/de78d5f7fdafaffb89a6272863840c5f.yaml -mcpu
[16:33:31] [Main        ] framework hash: vevev
[16:33:31] [Main        ] deployment mode: devel (True)
[16:33:31] [Main        ] Test Runner Setup - ""

[16:33:31] [Main        ] Using Teaser for data set creation
[16:33:31] [Teaser      ] Init. Creating 1 test datasets.
[16:33:32] [Teaser      ] 
[16:33:32] [Teaser      ] Creating test de78d5f7fdafaffb89a6272863840c5f
[16:33:32] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f
[16:33:32] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f
[16:33:32] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[16:33:32] [Teaser      ] csample /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 4500 0.500000
[16:33:32] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[16:33:32] [Teaser      ] Sampling as contig: 1350 regions of size 4500 (pad 900), totalling 6078552 base pairs
[16:33:32] [Teaser      ] Sampling 1350 regions
[16:33:32] [Teaser      ] 10%
[16:33:32] [Teaser      ] 20%
[16:33:32] [Teaser      ] 30%
[16:33:32] [Teaser      ] 40%
[16:33:32] [Teaser      ] 50%
[16:33:32] [Teaser      ] 60%
[16:33:32] [Teaser      ] 70%
[16:33:33] [Teaser      ] 80%
[16:33:33] [Teaser      ] 90%
[16:33:33] [Teaser      ] 100%
[16:33:34] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f
[16:33:34] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 50000 --mp  --ll 400 --le 50  --hi 0.006000  --hs 0.014000  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta
[16:33:34] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 50000 --mp  --ll 400 --le 50  --hi 0.006000  --hs 0.014000  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta
[16:34:31] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta_1.fastq -> ./reads1.fastq
[16:34:31] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta_2.fastq -> ./reads2.fastq
[16:34:31] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta.fastq.sam -> ./mapping_comparison.sam
[16:34:31] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f
[16:34:31] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[16:34:31] [Teaser      ] Translating SAM file coordinates (as contig)...
[16:34:31] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[16:34:48] [Teaser      ] remove /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta
[16:34:48] [Teaser      ] remove /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta.index
[16:34:48] [Teaser      ] remove mapping_comparison_unfixed.sam
[16:34:48] [Teaser      ] Took 76 seconds for generating de78d5f7fdafaffb89a6272863840c5f
[16:34:48] [Main        ] Data set creation completed
[16:34:48] [Main        ] 
[16:34:49] [bowtie2     ] de78d5f7fdafaffb89a6272863840c5f (base: tests_base/base_mapping)
[16:34:49] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[16:34:49] [init        ] Reads: /project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f/reads1.fastq
[16:34:49] [init        ] Output:/project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f/out_bowtie2.sam
[16:34:49] [map         ] Command(pre): 
[16:34:49] [map         ] Base run time file not existing, performing base run
[16:34:49] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
[16:34:53] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
[16:34:53] [map         ]    Mapping 32.00MB to 12.00MB with bowtie2...
[16:35:09] [map         ]    Took 15.791 (wall), 39.172 (CPU) seconds, initialization time: 2.668 (wall), 0.396 (CPU) seconds.
[16:35:09] [map         ] Command(post): 
[16:35:09] [sort_prepare] Sorting...
[16:35:20] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:35:33] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
98991,776,233,0,0,100000,0,0,0.992221876973,0.997651777796,0.994929418918

[16:35:33] [bwa         ] de78d5f7fdafaffb89a6272863840c5f (base: tests_base/base_mapping)
[16:35:33] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[16:35:33] [init        ] Reads: /project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f/reads1.fastq
[16:35:33] [init        ] Output:/project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f/out_bwa.sam
[16:35:33] [map         ] Command(pre): 
[16:35:33] [map         ] Base run time file not existing, performing base run
[16:35:33] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[16:35:36] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq  -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads2.fastq  -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
[16:35:36] [map         ]    Mapping 32.00MB to 12.00MB with bwa...
[16:36:20] [map         ]    Took 43.988 (wall), 48.124 (CPU) seconds, initialization time: 0.217 (wall), 0.056 (CPU) seconds.
[16:36:20] [map         ] Command(post): 
[16:36:23] [sort_prepare] Sorting...
[16:36:32] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:36:48] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
88406,585,11009,0,0,100000,0,0,0.993426301536,0.889262183775,0.938462681656

[16:36:53] [bwamem      ] de78d5f7fdafaffb89a6272863840c5f (base: tests_base/base_mapping)
[16:36:56] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[16:36:56] [init        ] Reads: /project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f/reads1.fastq
[16:36:56] [init        ] Output:/project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f/out_bwamem.sam
[16:36:59] [map         ] Command(pre): 
[16:37:00] [map         ] Base run time file not existing, performing base run
[16:37:01] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq  -t 4 > out_bwamem.sam
[16:37:25] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq  -t 4 > out_bwamem.sam
[16:37:25] [map         ]    Mapping 32.00MB to 12.00MB with bwamem...
[16:37:46] [map         ]    Took 19.578 (wall), 21.976 (CPU) seconds, initialization time: 8.555 (wall), 0.056 (CPU) seconds.
[16:37:46] [map         ] Command(post): 
[16:37:48] [sort_prepare] Sorting...
[16:37:59] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:38:13] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
99254,746,0,0,0,100000,0,0,0.99254,1.0,0.996256035011

[16:38:18] [bwasw       ] de78d5f7fdafaffb89a6272863840c5f (base: tests_base/base_mapping)
[16:38:21] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[16:38:21] [init        ] Reads: /project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f/reads1.fastq
[16:38:21] [init        ] Output:/project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f/out_bwasw.sam
[16:38:24] [map         ] Command(pre): 
[16:38:25] [map         ] Base run time file not existing, performing base run
[16:38:26] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq  -t 4 > out_bwasw.sam
[16:38:45] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq  -t 4 > out_bwasw.sam
[16:38:45] [map         ]    Mapping 32.00MB to 12.00MB with bwasw...
[16:39:23] [map         ]    Took 36.892 (wall), 85.720 (CPU) seconds, initialization time: 6.414 (wall), 0.052 (CPU) seconds.
[16:39:23] [map         ] Command(post): 
[16:39:28] [sort_prepare] Sorting...
[16:39:39] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:39:46] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
99066,934,0,0,1,100000,0,0,0.99066,1.0,0.995308088775

[16:39:54] [ngm         ] de78d5f7fdafaffb89a6272863840c5f (base: tests_base/base_mapping)
[16:39:56] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[16:39:56] [init        ] Reads: /project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f/reads1.fastq
[16:39:56] [init        ] Output:/project/teaser/genometeaser/tests_generated/de78d5f7fdafaffb89a6272863840c5f/out_ngm.sam
[16:39:59] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 
[16:40:08] [map         ] Base run time file not existing, performing base run
[16:40:09] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta -t 4 --qry reads_base.fastq  --no-progress
[16:40:32] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta -t 4  --no-progress
[16:40:32] [map         ]    Mapping 32.00MB to 12.00MB with ngm...
[16:40:46] [map         ]    Took 13.147 (wall), 16.736 (CPU) seconds, initialization time: 5.498 (wall), 3.200 (CPU) seconds.
[16:40:46] [map         ] Command(post): 
[16:40:46] [sort_prepare] Sorting...
[16:40:55] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:41:09] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
99203,797,0,0,0,100000,0,0,0.99203,1.0,0.995999056239