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
E_coliE_coli5500
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 Accessionf3cfc70a77888b8626def783d24d0e80
Report timestampWed Aug 22 19:21:32 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/f3cfc70a77888b8626def783d24d0e80.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 32}
include: [base_teaser.yaml]
meta_timestamp: 1534957910.518006
report: {name: f3cfc70a77888b8626def783d24d0e80}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    f3cfc70a77888b8626def783d24d0e80: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 150,
      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: 65,
      reference: !!python/unicode 'E_coli.fasta', title: !!python/unicode 'E_coli',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[19:11:54] [Main        ] framework cmd:  ./teaser.py setups_generated/f3cfc70a77888b8626def783d24d0e80.yaml -mcpu
[19:11:54] [Main        ] framework hash: vevev
[19:11:54] [Main        ] deployment mode: devel (True)
[19:11:54] [Main        ] Test Runner Setup - ""

[19:11:54] [Main        ] Using Teaser for data set creation
[19:11:54] [Teaser      ] Init. Creating 1 test datasets.
[19:11:54] [Teaser      ] 
[19:11:54] [Teaser      ] Creating test f3cfc70a77888b8626def783d24d0e80
[19:11:54] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80
[19:11:54] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80
[19:11:54] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/E_coli.fasta.teaser.findex
[19:11:54] [Teaser      ] csample /project/teaser/genometeaser/references/E_coli.fasta 2000 0.500000
[19:11:55] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/E_coli.fasta.teaser.findex
[19:11:55] [Teaser      ] Sampling as contig: 1283 regions of size 2000 (pad 400), totalling 2566034 base pairs
[19:11:55] [Teaser      ] Sampling 1283 regions
[19:11:56] [Teaser      ] 10%
[19:11:56] [Teaser      ] 20%
[19:11:56] [Teaser      ] 30%
[19:11:56] [Teaser      ] 40%
[19:11:57] [Teaser      ] 50%
[19:11:57] [Teaser      ] 60%
[19:11:57] [Teaser      ] 70%
[19:11:57] [Teaser      ] 80%
[19:11:57] [Teaser      ] 90%
[19:11:57] [Teaser      ] 100%
[19:11:58] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80
[19:11:58] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 65 -N 115384 --mp  --ll 150 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.2000.400.fasta
[19:11:58] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 65 -N 115384 --mp  --ll 150 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.2000.400.fasta
[19:13:06] [Teaser      ] move /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.2000.400.fasta_1.fastq -> ./reads1.fastq
[19:13:06] [Teaser      ] move /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.2000.400.fasta_2.fastq -> ./reads2.fastq
[19:13:06] [Teaser      ] move /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.2000.400.fasta.fastq.sam -> ./mapping_comparison.sam
[19:13:06] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80
[19:13:06] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[19:13:06] [Teaser      ] Translating SAM file coordinates (as contig)...
[19:13:06] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/E_coli.fasta.teaser.findex
[19:13:35] [Teaser      ] remove /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.2000.400.fasta
[19:13:35] [Teaser      ] remove /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.2000.400.fasta.index
[19:13:35] [Teaser      ] remove mapping_comparison_unfixed.sam
[19:13:35] [Teaser      ] Took 100 seconds for generating f3cfc70a77888b8626def783d24d0e80
[19:13:35] [Main        ] Data set creation completed
[19:13:35] [Main        ] 
[19:13:38] [bowtie2     ] f3cfc70a77888b8626def783d24d0e80 (base: tests_base/base_mapping)
[19:13:38] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[19:13:38] [init        ] Reads: /project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80/reads1.fastq
[19:13:38] [init        ] Output:/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80/out_bowtie2.sam
[19:13:38] [map         ] Command(pre): 
[19:13:38] [map         ] Base run time file not existing, performing base run
[19:13:38] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
[19:13:42] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
[19:13:42] [map         ]    Mapping 34.00MB to 5.00MB with bowtie2...
[19:14:15] [map         ]    Took 32.773 (wall), 73.848 (CPU) seconds, initialization time: 0.638 (wall), 0.616 (CPU) seconds.
[19:14:15] [map         ] Command(post): 
[19:14:15] [sort_prepare] Sorting...
[19:14:48] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 32)... 
[19:15:06] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
222996,7654,118,0,0,230768,0,0,0.966815521353,0.999471122386,0.982872153807

[19:15:06] [bwa         ] f3cfc70a77888b8626def783d24d0e80 (base: tests_base/base_mapping)
[19:15:06] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[19:15:06] [init        ] Reads: /project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80/reads1.fastq
[19:15:06] [init        ] Output:/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80/out_bwa.sam
[19:15:06] [map         ] Command(pre): 
[19:15:06] [map         ] Base run time file not existing, performing base run
[19:15:06] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/E_coli.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[19:15:09] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/E_coli.fasta reads1.fastq  -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/E_coli.fasta reads2.fastq  -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/E_coli.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
[19:15:09] [map         ]    Mapping 34.00MB to 5.00MB with bwa...
[19:16:12] [map         ]    Took 62.348 (wall), 70.812 (CPU) seconds, initialization time: 0.393 (wall), 0.084 (CPU) seconds.
[19:16:12] [map         ] Command(post): 
[19:16:12] [sort_prepare] Sorting...
[19:16:26] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 32)... 
[19:16:42] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
223010,7551,207,0,0,230768,0,0,0.967249448085,0.999072651277,0.982903534327

[19:16:43] [bwamem      ] f3cfc70a77888b8626def783d24d0e80 (base: tests_base/base_mapping)
[19:16:43] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[19:16:43] [init        ] Reads: /project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80/reads1.fastq
[19:16:43] [init        ] Output:/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80/out_bwamem.sam
[19:16:43] [map         ] Command(pre): 
[19:16:43] [map         ] Base run time file not existing, performing base run
[19:16:43] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq  -t 4 > out_bwamem.sam
[19:16:45] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads1.fastq reads2.fastq  -t 4 > out_bwamem.sam
[19:16:45] [map         ]    Mapping 34.00MB to 5.00MB with bwamem...
[19:17:19] [map         ]    Took 33.404 (wall), 51.272 (CPU) seconds, initialization time: 0.199 (wall), 0.064 (CPU) seconds.
[19:17:19] [map         ] Command(post): 
[19:17:19] [sort_prepare] Sorting...
[19:17:33] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 32)... 
[19:17:51] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
223121,7647,0,0,0,230768,0,0,0.966862823268,1.0,0.983152268506

[19:17:51] [bwasw       ] f3cfc70a77888b8626def783d24d0e80 (base: tests_base/base_mapping)
[19:17:51] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[19:17:51] [init        ] Reads: /project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80/reads1.fastq
[19:17:51] [init        ] Output:/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80/out_bwasw.sam
[19:17:51] [map         ] Command(pre): 
[19:17:51] [map         ] Base run time file not existing, performing base run
[19:17:51] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq  -t 4 > out_bwasw.sam
[19:17:53] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads1.fastq reads2.fastq  -t 4 > out_bwasw.sam
[19:17:53] [map         ]    Mapping 34.00MB to 5.00MB with bwasw...
[19:18:57] [map         ]    Took 64.022 (wall), 168.912 (CPU) seconds, initialization time: 0.133 (wall), 0.060 (CPU) seconds.
[19:18:57] [map         ] Command(post): 
[19:18:57] [sort_prepare] Sorting...
[19:19:10] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 32)... 
[19:19:27] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
222465,8265,38,0,14,230768,0,0,0.964178910415,0.999829215786,0.981680504288

[19:19:27] [ngm         ] f3cfc70a77888b8626def783d24d0e80 (base: tests_base/base_mapping)
[19:19:27] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[19:19:27] [init        ] Reads: /project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80/reads1.fastq
[19:19:27] [init        ] Output:/project/teaser/genometeaser/tests_generated/f3cfc70a77888b8626def783d24d0e80/out_ngm.sam
[19:19:27] [map         ] Command(pre): 
[19:19:27] [map         ] Base run time file not existing, performing base run
[19:19:27] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/E_coli.fasta -t 4 --qry reads_base.fastq  --no-progress
[19:20:28] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/E_coli.fasta -t 4  --no-progress
[19:20:28] [map         ]    Mapping 34.00MB to 5.00MB with ngm...
[19:21:02] [map         ]    Took 32.235 (wall), 41.296 (CPU) seconds, initialization time: 9.159 (wall), 8.432 (CPU) seconds.
[19:21:02] [map         ] Command(post): 
[19:21:02] [sort_prepare] Sorting...
[19:21:15] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 32)... 
[19:21:32] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
223148,7620,0,0,0,230768,0,0,0.966979823892,1.0,0.98321275302