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 Accessiona1196814bed1e8498427aa17a7703943
Report timestampWed May 17 13:47:19 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/a1196814bed1e8498427aa17a7703943.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1495021478.729322
report: {name: a1196814bed1e8498427aa17a7703943}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    a1196814bed1e8498427aa17a7703943: {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: 0.001, paired: true, platform: !!python/unicode 'illumina', read_length: 60,
      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
[13:44:40] [Main        ] framework cmd:  ./teaser.py setups_generated/a1196814bed1e8498427aa17a7703943.yaml -mcpu
[13:44:40] [Main        ] framework hash: vevev
[13:44:40] [Main        ] deployment mode: devel (True)
[13:44:40] [Main        ] Test Runner Setup - ""

[13:44:40] [Main        ] Using Teaser for data set creation
[13:44:40] [Teaser      ] Init. Creating 1 test datasets.
[13:44:40] [Teaser      ] 
[13:44:40] [Teaser      ] Creating test a1196814bed1e8498427aa17a7703943
[13:44:40] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943
[13:44:40] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943
[13:44:40] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[13:44:40] [Teaser      ] csample /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 1500 0.500000
[13:44:40] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[13:44:40] [Teaser      ] Sampling as contig: 4052 regions of size 1500 (pad 300), totalling 6078552 base pairs
[13:44:40] [Teaser      ] Sampling 4052 regions
[13:44:40] [Teaser      ] 10%
[13:44:41] [Teaser      ] 20%
[13:44:41] [Teaser      ] 30%
[13:44:41] [Teaser      ] 40%
[13:44:41] [Teaser      ] 50%
[13:44:41] [Teaser      ] 60%
[13:44:41] [Teaser      ] 70%
[13:44:41] [Teaser      ] 80%
[13:44:42] [Teaser      ] 90%
[13:44:42] [Teaser      ] 100%
[13:44:42] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943
[13:44:42] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 125000 --mp  --ll 100 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.1500.300.fasta
[13:44:42] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 125000 --mp  --ll 100 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.1500.300.fasta
[13:45:04] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.1500.300.fasta_1.fastq -> ./reads1.fastq
[13:45:04] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.1500.300.fasta_2.fastq -> ./reads2.fastq
[13:45:04] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.1500.300.fasta.fastq.sam -> ./mapping_comparison.sam
[13:45:04] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943
[13:45:04] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[13:45:04] [Teaser      ] Translating SAM file coordinates (as contig)...
[13:45:04] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[13:45:16] [Teaser      ] remove /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.1500.300.fasta
[13:45:16] [Teaser      ] remove /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.1500.300.fasta.index
[13:45:16] [Teaser      ] remove mapping_comparison_unfixed.sam
[13:45:16] [Teaser      ] Took 35 seconds for generating a1196814bed1e8498427aa17a7703943
[13:45:16] [Main        ] Data set creation completed
[13:45:16] [Main        ] 
[13:45:16] [bowtie2     ] a1196814bed1e8498427aa17a7703943 (base: tests_base/base_mapping)
[13:45:16] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[13:45:16] [init        ] Reads: /project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943/reads1.fastq
[13:45:16] [init        ] Output:/project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943/out_bowtie2.sam
[13:45:16] [map         ] Command(pre): 
[13:45:16] [map         ] Base run time file not existing, performing base run
[13:45:16] [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
[13:45:18] [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
[13:45:18] [map         ]    Mapping 35.00MB to 12.00MB with bowtie2...
[13:45:27] [map         ]    Took 8.854 (wall), 30.088 (CPU) seconds, initialization time: 0.220 (wall), 0.244 (CPU) seconds.
[13:45:27] [map         ] Command(post): 
[13:45:27] [sort_prepare] Sorting...
[13:45:32] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[13:45:40] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
246542,3270,188,0,0,250000,0,0,0.986910156438,0.999238033478,0.993035835841

[13:45:41] [bwa         ] a1196814bed1e8498427aa17a7703943 (base: tests_base/base_mapping)
[13:45:41] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[13:45:41] [init        ] Reads: /project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943/reads1.fastq
[13:45:41] [init        ] Output:/project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943/out_bwa.sam
[13:45:41] [map         ] Command(pre): 
[13:45:41] [map         ] Base run time file not existing, performing base run
[13:45:41] [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
[13:45:43] [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
[13:45:43] [map         ]    Mapping 35.00MB to 12.00MB with bwa...
[13:45:54] [map         ]    Took 10.007 (wall), 19.416 (CPU) seconds, initialization time: 0.113 (wall), 0.041 (CPU) seconds.
[13:45:54] [map         ] Command(post): 
[13:45:54] [sort_prepare] Sorting...
[13:45:56] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[13:46:03] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
245748,3276,976,0,0,250000,0,0,0.98684464148,0.996044162708,0.991423061717

[13:46:04] [bwamem      ] a1196814bed1e8498427aa17a7703943 (base: tests_base/base_mapping)
[13:46:04] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[13:46:04] [init        ] Reads: /project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943/reads1.fastq
[13:46:04] [init        ] Output:/project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943/out_bwamem.sam
[13:46:04] [map         ] Command(pre): 
[13:46:04] [map         ] Base run time file not existing, performing base run
[13:46:04] [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
[13:46:06] [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
[13:46:06] [map         ]    Mapping 35.00MB to 12.00MB with bwamem...
[13:46:11] [map         ]    Took 4.095 (wall), 11.323 (CPU) seconds, initialization time: 0.057 (wall), 0.023 (CPU) seconds.
[13:46:11] [map         ] Command(post): 
[13:46:11] [sort_prepare] Sorting...
[13:46:13] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[13:46:21] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
246811,3189,0,0,0,250000,0,0,0.987244,1.0,0.993581060001

[13:46:21] [bwasw       ] a1196814bed1e8498427aa17a7703943 (base: tests_base/base_mapping)
[13:46:21] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[13:46:21] [init        ] Reads: /project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943/reads1.fastq
[13:46:21] [init        ] Output:/project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943/out_bwasw.sam
[13:46:21] [map         ] Command(pre): 
[13:46:21] [map         ] Base run time file not existing, performing base run
[13:46:21] [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
[13:46:23] [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
[13:46:23] [map         ]    Mapping 35.00MB to 12.00MB with bwasw...
[13:46:46] [map         ]    Took 22.156 (wall), 70.319 (CPU) seconds, initialization time: 0.258 (wall), 0.024 (CPU) seconds.
[13:46:46] [map         ] Command(post): 
[13:46:46] [sort_prepare] Sorting...
[13:46:48] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[13:46:56] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
246086,3645,269,0,2,250000,0,0,0.985404295021,0.998908079804,0.992110238951

[13:46:56] [ngm         ] a1196814bed1e8498427aa17a7703943 (base: tests_base/base_mapping)
[13:46:56] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[13:46:56] [init        ] Reads: /project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943/reads1.fastq
[13:46:56] [init        ] Output:/project/teaser/genometeaser/tests_generated/a1196814bed1e8498427aa17a7703943/out_ngm.sam
[13:46:56] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 
[13:47:00] [map         ] Base run time file not existing, performing base run
[13:47:00] [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
[13:47:04] [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
[13:47:04] [map         ]    Mapping 35.00MB to 12.00MB with ngm...
[13:47:09] [map         ]    Took 4.692 (wall), 10.627 (CPU) seconds, initialization time: 1.837 (wall), 2.204 (CPU) seconds.
[13:47:09] [map         ] Command(post): 
[13:47:09] [sort_prepare] Sorting...
[13:47:11] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[13:47:19] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
246709,3291,0,0,0,250000,0,0,0.986836,1.0,0.993374390237