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 Accession316281ab4f84058f3c27332d7303df8f
Report timestampFri Aug 24 14:56:46 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/316281ab4f84058f3c27332d7303df8f.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 25}
include: [base_teaser.yaml]
meta_timestamp: 1535113947.080575
report: {name: 316281ab4f84058f3c27332d7303df8f}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    316281ab4f84058f3c27332d7303df8f: {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
[14:33:14] [Main        ] framework cmd:  ./teaser.py setups_generated/316281ab4f84058f3c27332d7303df8f.yaml -mcpu
[14:33:14] [Main        ] framework hash: vevev
[14:33:14] [Main        ] deployment mode: devel (True)
[14:33:14] [Main        ] Test Runner Setup - ""

[14:33:15] [Main        ] Using Teaser for data set creation
[14:33:16] [Teaser      ] Init. Creating 1 test datasets.
[14:33:16] [Teaser      ] 
[14:33:16] [Teaser      ] Creating test 316281ab4f84058f3c27332d7303df8f
[14:33:16] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f
[14:33:16] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f
[14:33:16] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[14:33:16] [Teaser      ] csample /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 500 0.500000
[14:33:19] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[14:33:19] [Teaser      ] Sampling as contig: 12157 regions of size 500 (pad 100), totalling 6078552 base pairs
[14:33:19] [Teaser      ] Sampling 12157 regions
[14:33:28] [Teaser      ] 10%
[14:33:43] [Teaser      ] 20%
[14:33:45] [Teaser      ] 30%
[14:33:47] [Teaser      ] 40%
[14:33:49] [Teaser      ] 50%
[14:33:50] [Teaser      ] 60%
[14:33:52] [Teaser      ] 70%
[14:33:54] [Teaser      ] 80%
[14:33:56] [Teaser      ] 90%
[14:33:58] [Teaser      ] 100%
[14:34:06] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f
[14:34:06] [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
[14:34:06] [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
[14:35:22] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.500.100.fasta.fastq -> ./reads.fastq
[14:35:22] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.500.100.fasta.fastq.sam -> ./mapping_comparison.sam
[14:35:22] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f
[14:35:22] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[14:35:22] [Teaser      ] Translating SAM file coordinates (as contig)...
[14:35:22] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[14:36:36] [Teaser      ] remove /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.500.100.fasta
[14:36:37] [Teaser      ] remove /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.500.100.fasta.index
[14:36:37] [Teaser      ] remove mapping_comparison_unfixed.sam
[14:36:37] [Teaser      ] Took 200 seconds for generating 316281ab4f84058f3c27332d7303df8f
[14:36:38] [Main        ] Data set creation completed
[14:36:38] [Main        ] 
[14:37:30] [bowtie2     ] 316281ab4f84058f3c27332d7303df8f (base: tests_base/base_mapping)
[14:37:30] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[14:37:30] [init        ] Reads: /project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f/reads.fastq
[14:37:30] [init        ] Output:/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f/out_bowtie2.sam
[14:37:30] [map         ] Command(pre): 
[14:37:30] [map         ] Base run time file not existing, performing base run
[14:37:30] [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
[14:39:02] [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
[14:39:02] [map         ]    Mapping 36.00MB to 12.00MB with bowtie2...
[14:41:28] [map         ]    Took 145.125 (wall), 66.956 (CPU) seconds, initialization time: 41.406 (wall), 0.352 (CPU) seconds.
[14:41:28] [map         ] Command(post): 
[14:41:28] [sort_prepare] Sorting...
[14:42:53] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:43:50] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
292398,5219,2383,0,0,300000,0,0,0.982464039353,0.99191603258,0.987167411099

[14:43:52] [bwa         ] 316281ab4f84058f3c27332d7303df8f (base: tests_base/base_mapping)
[14:43:53] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[14:43:53] [init        ] Reads: /project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f/reads.fastq
[14:43:53] [init        ] Output:/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f/out_bwa.sam
[14:43:53] [map         ] Command(pre): 
[14:43:53] [map         ] Base run time file not existing, performing base run
[14:43:53] [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
[14:44:40] [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
[14:44:40] [map         ]    Mapping 36.00MB to 12.00MB with bwa...
[14:46:08] [map         ]    Took 87.469 (wall), 63.312 (CPU) seconds, initialization time: 0.348 (wall), 0.132 (CPU) seconds.
[14:46:08] [map         ] Command(post): 
[14:46:08] [sort_prepare] Sorting...
[14:46:47] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:47:20] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
292379,5152,2469,0,0,300000,0,0,0.982684157281,0.991626193835,0.987134925445

[14:47:20] [bwamem      ] 316281ab4f84058f3c27332d7303df8f (base: tests_base/base_mapping)
[14:47:20] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[14:47:20] [init        ] Reads: /project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f/reads.fastq
[14:47:20] [init        ] Output:/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f/out_bwamem.sam
[14:47:20] [map         ] Command(pre): 
[14:47:21] [map         ] Base run time file not existing, performing base run
[14:47:21] [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
[14:47:30] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq  -t 4 > out_bwamem.sam
[14:47:30] [map         ]    Mapping 36.00MB to 12.00MB with bwamem...
[14:48:02] [map         ]    Took 31.481 (wall), 46.508 (CPU) seconds, initialization time: 7.664 (wall), 0.076 (CPU) seconds.
[14:48:02] [map         ] Command(post): 
[14:48:02] [sort_prepare] Sorting...
[14:48:35] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:49:00] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
294403,5231,366,0,0,300000,0,0,0.982542034616,0.998758349759,0.990583829489

[14:49:01] [bwasw       ] 316281ab4f84058f3c27332d7303df8f (base: tests_base/base_mapping)
[14:49:01] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[14:49:01] [init        ] Reads: /project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f/reads.fastq
[14:49:01] [init        ] Output:/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f/out_bwasw.sam
[14:49:01] [map         ] Command(pre): 
[14:49:01] [map         ] Base run time file not existing, performing base run
[14:49:01] [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
[14:49:07] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq  -t 4 > out_bwasw.sam
[14:49:07] [map         ]    Mapping 36.00MB to 12.00MB with bwasw...
[14:50:24] [map         ]    Took 76.841 (wall), 153.468 (CPU) seconds, initialization time: 0.419 (wall), 0.100 (CPU) seconds.
[14:50:24] [map         ] Command(post): 
[14:50:24] [sort_prepare] Sorting...
[14:51:01] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:51:37] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
280455,5025,14520,0,0,300000,0,0,0.982398066414,0.950775489448,0.966328139132

[14:51:38] [ngm         ] 316281ab4f84058f3c27332d7303df8f (base: tests_base/base_mapping)
[14:51:38] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[14:51:38] [init        ] Reads: /project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f/reads.fastq
[14:51:38] [init        ] Output:/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f/out_ngm.sam
[14:51:38] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 
[14:53:29] [map         ] Base run time file not existing, performing base run
[14:53:29] [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
[14:54:21] [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
[14:54:21] [map         ]    Mapping 36.00MB to 12.00MB with ngm...
[14:55:00] [map         ]    Took 38.758 (wall), 42.228 (CPU) seconds, initialization time: 23.961 (wall), 8.536 (CPU) seconds.
[14:55:00] [map         ] Command(post): 
[14:55:00] [sort_prepare] Sorting...
[14:55:52] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:56:45] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
294717,5276,7,0,0,300000,0,0,0.982412922968,0.999976248965,0.991116783277