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 Accessionbc5e667ff41f75be5690d71ac8911c05
Report timestampWed Oct 3 17:15:27 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/bc5e667ff41f75be5690d71ac8911c05.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 75}
include: [base_teaser.yaml]
meta_timestamp: 1538579360.530092
report: {name: bc5e667ff41f75be5690d71ac8911c05}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    bc5e667ff41f75be5690d71ac8911c05: {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
[17:09:21] [Main        ] framework cmd:  ./teaser.py setups_generated/bc5e667ff41f75be5690d71ac8911c05.yaml -mcpu
[17:09:21] [Main        ] framework hash: vevev
[17:09:21] [Main        ] deployment mode: devel (True)
[17:09:21] [Main        ] Test Runner Setup - ""

[17:09:22] [Main        ] Using Teaser for data set creation
[17:09:22] [Teaser      ] Init. Creating 1 test datasets.
[17:09:22] [Teaser      ] 
[17:09:22] [Teaser      ] Creating test bc5e667ff41f75be5690d71ac8911c05
[17:09:22] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05
[17:09:22] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05
[17:09:22] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[17:09:22] [Teaser      ] csample /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 4500 0.500000
[17:09:22] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[17:09:22] [Teaser      ] Sampling as contig: 1350 regions of size 4500 (pad 900), totalling 6078552 base pairs
[17:09:22] [Teaser      ] Sampling 1350 regions
[17:09:22] [Teaser      ] 10%
[17:09:22] [Teaser      ] 20%
[17:09:22] [Teaser      ] 30%
[17:09:22] [Teaser      ] 40%
[17:09:22] [Teaser      ] 50%
[17:09:23] [Teaser      ] 60%
[17:09:23] [Teaser      ] 70%
[17:09:23] [Teaser      ] 80%
[17:09:23] [Teaser      ] 90%
[17:09:23] [Teaser      ] 100%
[17:09:24] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05
[17:09:24] [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
[17:09:24] [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
[17:11:24] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta_1.fastq -> ./reads1.fastq
[17:11:24] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta_2.fastq -> ./reads2.fastq
[17:11:24] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta.fastq.sam -> ./mapping_comparison.sam
[17:11:24] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05
[17:11:24] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[17:11:24] [Teaser      ] Translating SAM file coordinates (as contig)...
[17:11:24] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[17:11:38] [Teaser      ] remove /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta
[17:11:39] [Teaser      ] remove /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta.index
[17:11:39] [Teaser      ] remove mapping_comparison_unfixed.sam
[17:11:39] [Teaser      ] Took 136 seconds for generating bc5e667ff41f75be5690d71ac8911c05
[17:11:39] [Main        ] Data set creation completed
[17:11:39] [Main        ] 
[17:11:39] [bowtie2     ] bc5e667ff41f75be5690d71ac8911c05 (base: tests_base/base_mapping)
[17:11:39] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[17:11:39] [init        ] Reads: /project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05/reads1.fastq
[17:11:39] [init        ] Output:/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05/out_bowtie2.sam
[17:11:39] [map         ] Command(pre): 
[17:11:39] [map         ] Base run time file not existing, performing base run
[17:11:39] [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
[17:11:42] [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
[17:11:42] [map         ]    Mapping 32.00MB to 12.00MB with bowtie2...
[17:11:54] [map         ]    Took 11.945 (wall), 31.500 (CPU) seconds, initialization time: 0.348 (wall), 0.400 (CPU) seconds.
[17:11:54] [map         ] Command(post): 
[17:11:54] [sort_prepare] Sorting...
[17:12:05] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[17:12:19] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
99063,706,231,0,0,100000,0,0,0.99292365364,0.997673575443,0.995292947459

[17:12:19] [bwa         ] bc5e667ff41f75be5690d71ac8911c05 (base: tests_base/base_mapping)
[17:12:19] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[17:12:19] [init        ] Reads: /project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05/reads1.fastq
[17:12:19] [init        ] Output:/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05/out_bwa.sam
[17:12:19] [map         ] Command(pre): 
[17:12:19] [map         ] Base run time file not existing, performing base run
[17:12:19] [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
[17:12:21] [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
[17:12:21] [map         ]    Mapping 32.00MB to 12.00MB with bwa...
[17:12:56] [map         ]    Took 34.006 (wall), 48.752 (CPU) seconds, initialization time: 0.176 (wall), 0.060 (CPU) seconds.
[17:12:56] [map         ] Command(post): 
[17:12:56] [sort_prepare] Sorting...
[17:13:01] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[17:13:14] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
88402,591,11007,0,0,100000,0,0,0.993359028238,0.889275618908,0.938440143948

[17:13:14] [bwamem      ] bc5e667ff41f75be5690d71ac8911c05 (base: tests_base/base_mapping)
[17:13:14] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[17:13:14] [init        ] Reads: /project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05/reads1.fastq
[17:13:14] [init        ] Output:/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05/out_bwamem.sam
[17:13:14] [map         ] Command(pre): 
[17:13:14] [map         ] Base run time file not existing, performing base run
[17:13:14] [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
[17:13:16] [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
[17:13:16] [map         ]    Mapping 32.00MB to 12.00MB with bwamem...
[17:13:27] [map         ]    Took 9.391 (wall), 21.624 (CPU) seconds, initialization time: 0.111 (wall), 0.048 (CPU) seconds.
[17:13:27] [map         ] Command(post): 
[17:13:27] [sort_prepare] Sorting...
[17:13:31] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[17:13:45] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
99260,740,0,0,0,100000,0,0,0.9926,1.0,0.996286259159

[17:13:45] [bwasw       ] bc5e667ff41f75be5690d71ac8911c05 (base: tests_base/base_mapping)
[17:13:45] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[17:13:45] [init        ] Reads: /project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05/reads1.fastq
[17:13:45] [init        ] Output:/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05/out_bwasw.sam
[17:13:45] [map         ] Command(pre): 
[17:13:45] [map         ] Base run time file not existing, performing base run
[17:13:45] [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
[17:13:47] [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
[17:13:47] [map         ]    Mapping 32.00MB to 12.00MB with bwasw...
[17:14:31] [map         ]    Took 43.654 (wall), 91.220 (CPU) seconds, initialization time: 0.117 (wall), 0.048 (CPU) seconds.
[17:14:31] [map         ] Command(post): 
[17:14:31] [sort_prepare] Sorting...
[17:14:36] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[17:14:49] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
99093,907,0,0,0,100000,0,0,0.99093,1.0,0.995444340082

[17:14:49] [ngm         ] bc5e667ff41f75be5690d71ac8911c05 (base: tests_base/base_mapping)
[17:14:49] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[17:14:49] [init        ] Reads: /project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05/reads1.fastq
[17:14:49] [init        ] Output:/project/teaser/genometeaser/tests_generated/bc5e667ff41f75be5690d71ac8911c05/out_ngm.sam
[17:14:49] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 
[17:14:50] [map         ] Base run time file not existing, performing base run
[17:14:50] [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
[17:14:57] [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
[17:14:57] [map         ]    Mapping 32.00MB to 12.00MB with ngm...
[17:15:08] [map         ]    Took 10.814 (wall), 19.136 (CPU) seconds, initialization time: 2.941 (wall), 3.096 (CPU) seconds.
[17:15:08] [map         ] Command(post): 
[17:15:08] [sort_prepare] Sorting...
[17:15:13] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[17:15:27] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
99190,810,0,0,0,100000,0,0,0.9919,1.0,0.9959335308