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 Accession50d3e669ec8fd54ec3ae5364036f143a
Report timestampFri Jul 27 20:21:59 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/50d3e669ec8fd54ec3ae5364036f143a.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 25}
include: [base_teaser.yaml]
meta_timestamp: 1532715298.981354
report: {name: 50d3e669ec8fd54ec3ae5364036f143a}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    50d3e669ec8fd54ec3ae5364036f143a: {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: 50, 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
[20:15:00] [Main        ] framework cmd:  ./teaser.py setups_generated/50d3e669ec8fd54ec3ae5364036f143a.yaml -mcpu
[20:15:00] [Main        ] framework hash: vevev
[20:15:00] [Main        ] deployment mode: devel (True)
[20:15:00] [Main        ] Test Runner Setup - ""

[20:15:00] [Main        ] Using Teaser for data set creation
[20:15:01] [Teaser      ] Init. Creating 1 test datasets.
[20:15:01] [Teaser      ] 
[20:15:01] [Teaser      ] Creating test 50d3e669ec8fd54ec3ae5364036f143a
[20:15:01] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a
[20:15:01] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a
[20:15:01] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[20:15:01] [Teaser      ] csample /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 500 0.500000
[20:15:01] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[20:15:01] [Teaser      ] Sampling as contig: 12157 regions of size 500 (pad 100), totalling 6078552 base pairs
[20:15:01] [Teaser      ] Sampling 12157 regions
[20:15:03] [Teaser      ] 10%
[20:15:04] [Teaser      ] 20%
[20:15:05] [Teaser      ] 30%
[20:15:06] [Teaser      ] 40%
[20:15:08] [Teaser      ] 50%
[20:15:09] [Teaser      ] 60%
[20:15:10] [Teaser      ] 70%
[20:15:12] [Teaser      ] 80%
[20:15:14] [Teaser      ] 90%
[20:15:16] [Teaser      ] 100%
[20:15:17] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a
[20:15:17] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 50 -N 300000  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.500.100.fasta
[20:15:17] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 50 -N 300000  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.500.100.fasta
[20:15:53] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.500.100.fasta.fastq -> ./reads.fastq
[20:15:53] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.500.100.fasta.fastq.sam -> ./mapping_comparison.sam
[20:15:53] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a
[20:15:53] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[20:15:53] [Teaser      ] Translating SAM file coordinates (as contig)...
[20:15:53] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[20:16:31] [Teaser      ] remove /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.500.100.fasta
[20:16:31] [Teaser      ] remove /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.500.100.fasta.index
[20:16:31] [Teaser      ] remove mapping_comparison_unfixed.sam
[20:16:31] [Teaser      ] Took 90 seconds for generating 50d3e669ec8fd54ec3ae5364036f143a
[20:16:32] [Main        ] Data set creation completed
[20:16:32] [Main        ] 
[20:16:32] [bowtie2     ] 50d3e669ec8fd54ec3ae5364036f143a (base: tests_base/base_mapping)
[20:16:32] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[20:16:32] [init        ] Reads: /project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a/reads.fastq
[20:16:32] [init        ] Output:/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a/out_bowtie2.sam
[20:16:32] [map         ] Command(pre): 
[20:16:32] [map         ] Base run time file not existing, performing base run
[20:16:32] [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
[20:16:37] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads.fastq -S out_bowtie2.sam
[20:16:37] [map         ]    Mapping 36.00MB to 12.00MB with bowtie2...
[20:16:48] [map         ]    Took 10.629 (wall), 20.612 (CPU) seconds, initialization time: 0.351 (wall), 0.392 (CPU) seconds.
[20:16:48] [map         ] Command(post): 
[20:16:48] [sort_prepare] Sorting...
[20:17:10] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[20:17:36] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
292633,4947,2420,0,0,300000,0,0,0.983375898918,0.991798083734,0.987569035136

[20:17:36] [bwa         ] 50d3e669ec8fd54ec3ae5364036f143a (base: tests_base/base_mapping)
[20:17:36] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[20:17:36] [init        ] Reads: /project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a/reads.fastq
[20:17:36] [init        ] Output:/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a/out_bwa.sam
[20:17:36] [map         ] Command(pre): 
[20:17:36] [map         ] Base run time file not existing, performing base run
[20:17:36] [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
[20:17:41] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.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.fastq > out_bwa.sam
[20:17:41] [map         ]    Mapping 36.00MB to 12.00MB with bwa...
[20:18:04] [map         ]    Took 22.026 (wall), 29.996 (CPU) seconds, initialization time: 0.155 (wall), 0.064 (CPU) seconds.
[20:18:04] [map         ] Command(post): 
[20:18:04] [sort_prepare] Sorting...
[20:18:12] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[20:18:37] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
292474,5065,2461,0,0,300000,0,0,0.9829770215,0.991655788564,0.987297332879

[20:18:37] [bwamem      ] 50d3e669ec8fd54ec3ae5364036f143a (base: tests_base/base_mapping)
[20:18:37] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[20:18:37] [init        ] Reads: /project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a/reads.fastq
[20:18:37] [init        ] Output:/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a/out_bwamem.sam
[20:18:37] [map         ] Command(pre): 
[20:18:37] [map         ] Base run time file not existing, performing base run
[20:18:37] [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
[20:18:39] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq  -t 4 > out_bwamem.sam
[20:18:39] [map         ]    Mapping 36.00MB to 12.00MB with bwamem...
[20:18:48] [map         ]    Took 8.326 (wall), 13.448 (CPU) seconds, initialization time: 0.102 (wall), 0.048 (CPU) seconds.
[20:18:48] [map         ] Command(post): 
[20:18:48] [sort_prepare] Sorting...
[20:18:55] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[20:19:19] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
294612,5036,352,0,0,300000,0,0,0.98319361384,0.99880663403,0.990938628887

[20:19:19] [bwasw       ] 50d3e669ec8fd54ec3ae5364036f143a (base: tests_base/base_mapping)
[20:19:20] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[20:19:20] [init        ] Reads: /project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a/reads.fastq
[20:19:20] [init        ] Output:/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a/out_bwasw.sam
[20:19:20] [map         ] Command(pre): 
[20:19:20] [map         ] Base run time file not existing, performing base run
[20:19:20] [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
[20:19:22] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq  -t 4 > out_bwasw.sam
[20:19:22] [map         ]    Mapping 36.00MB to 12.00MB with bwasw...
[20:20:02] [map         ]    Took 39.015 (wall), 97.496 (CPU) seconds, initialization time: 0.118 (wall), 0.048 (CPU) seconds.
[20:20:02] [map         ] Command(post): 
[20:20:02] [sort_prepare] Sorting...
[20:20:09] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[20:20:33] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
280742,4760,14498,0,0,300000,0,0,0.983327612416,0.950894187779,0.966838974967

[20:20:33] [ngm         ] 50d3e669ec8fd54ec3ae5364036f143a (base: tests_base/base_mapping)
[20:20:33] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[20:20:33] [init        ] Reads: /project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a/reads.fastq
[20:20:33] [init        ] Output:/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a/out_ngm.sam
[20:20:33] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 
[20:21:05] [map         ] Base run time file not existing, performing base run
[20:21:05] [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
[20:21:13] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta -t 4 --qry reads.fastq  --no-progress
[20:21:13] [map         ]    Mapping 36.00MB to 12.00MB with ngm...
[20:21:26] [map         ]    Took 12.909 (wall), 18.520 (CPU) seconds, initialization time: 3.329 (wall), 3.668 (CPU) seconds.
[20:21:26] [map         ] Command(post): 
[20:21:26] [sort_prepare] Sorting...
[20:21:34] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[20:21:59] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
294841,5151,8,0,0,300000,0,0,0.982829542121,0.999972867468,0.991327094131