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 Accession4c21a44c9042d3b44a6729ccaaa2740e
Report timestampMon Oct 22 17:24:46 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/4c21a44c9042d3b44a6729ccaaa2740e.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 225}
include: [base_teaser.yaml]
meta_timestamp: 1540221337.74969
report: {name: 4c21a44c9042d3b44a6729ccaaa2740e}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    4c21a44c9042d3b44a6729ccaaa2740e: {coverage: 1.0, error_rate_mult: 1.0, mutation_indel_avg_len: 3.0,
      mutation_indel_frac: 0.3, mutation_rate: 0.035, paired: false, platform: !!python/unicode 'illumina',
      read_length: 450, 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
[17:15:40] [Main        ] framework cmd:  ./teaser.py setups_generated/4c21a44c9042d3b44a6729ccaaa2740e.yaml -mcpu
[17:15:40] [Main        ] framework hash: vevev
[17:15:40] [Main        ] deployment mode: devel (True)
[17:15:40] [Main        ] Test Runner Setup - ""

[17:15:40] [Main        ] Using Teaser for data set creation
[17:15:40] [Teaser      ] Init. Creating 1 test datasets.
[17:15:41] [Teaser      ] 
[17:15:41] [Teaser      ] Creating test 4c21a44c9042d3b44a6729ccaaa2740e
[17:15:41] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e
[17:15:41] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e
[17:15:41] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/E_coli.fasta.teaser.findex
[17:15:41] [Teaser      ] csample /project/teaser/genometeaser/references/E_coli.fasta 4500 0.500000
[17:15:41] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/E_coli.fasta.teaser.findex
[17:15:41] [Teaser      ] Sampling as contig: 570 regions of size 4500 (pad 900), totalling 2566034 base pairs
[17:15:41] [Teaser      ] Sampling 570 regions
[17:15:41] [Teaser      ] 10%
[17:15:41] [Teaser      ] 20%
[17:15:41] [Teaser      ] 30%
[17:15:41] [Teaser      ] 40%
[17:15:41] [Teaser      ] 50%
[17:15:41] [Teaser      ] 60%
[17:15:42] [Teaser      ] 70%
[17:15:42] [Teaser      ] 80%
[17:15:42] [Teaser      ] 90%
[17:15:42] [Teaser      ] 100%
[17:15:42] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e
[17:15:42] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 450 -N 33333  --ll 500 --le 50  --hi 0.010500  --hs 0.024500  --hm 1 --hM 8 --source-no-N  /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.4500.900.fasta
[17:15:42] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 450 -N 33333  --ll 500 --le 50  --hi 0.010500  --hs 0.024500  --hm 1 --hM 8 --source-no-N  /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.4500.900.fasta
[17:20:58] [Teaser      ] move /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.4500.900.fasta.fastq -> ./reads.fastq
[17:20:58] [Teaser      ] move /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.4500.900.fasta.fastq.sam -> ./mapping_comparison.sam
[17:20:58] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e
[17:20:58] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[17:20:58] [Teaser      ] Translating SAM file coordinates (as contig)...
[17:20:58] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/E_coli.fasta.teaser.findex
[17:21:05] [Teaser      ] remove /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.4500.900.fasta
[17:21:05] [Teaser      ] remove /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.4500.900.fasta.index
[17:21:05] [Teaser      ] remove mapping_comparison_unfixed.sam
[17:21:05] [Teaser      ] Took 325 seconds for generating 4c21a44c9042d3b44a6729ccaaa2740e
[17:21:06] [Main        ] Data set creation completed
[17:21:06] [Main        ] 
[17:21:08] [bowtie2     ] 4c21a44c9042d3b44a6729ccaaa2740e (base: tests_base/base_mapping)
[17:21:08] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[17:21:08] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e/reads.fastq
[17:21:08] [init        ] Output:/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e/out_bowtie2.sam
[17:21:08] [map         ] Command(pre): 
[17:21:08] [map         ] Base run time file not existing, performing base run
[17:21:08] [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
[17:21:12] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -U reads.fastq -S out_bowtie2.sam
[17:21:12] [map         ]    Mapping 30.00MB to 5.00MB with bowtie2...
[17:21:32] [map         ]    Took 19.231 (wall), 63.188 (CPU) seconds, initialization time: 0.342 (wall), 0.408 (CPU) seconds.
[17:21:32] [map         ] Command(post): 
[17:21:32] [sort_prepare] Sorting...
[17:21:41] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 225)... 
[17:21:52] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
32388,936,9,0,0,33333,0,0,0.971912135398,0.9997221965,0.985621034373

[17:21:52] [bwa         ] 4c21a44c9042d3b44a6729ccaaa2740e (base: tests_base/base_mapping)
[17:21:52] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[17:21:52] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e/reads.fastq
[17:21:52] [init        ] Output:/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e/out_bwa.sam
[17:21:52] [map         ] Command(pre): 
[17:21:52] [map         ] Base run time file not existing, performing base run
[17:21:52] [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
[17:21:55] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/E_coli.fasta reads.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.fastq > out_bwa.sam
[17:21:55] [map         ]    Mapping 30.00MB to 5.00MB with bwa...
[17:22:02] [map         ]    Took 6.268 (wall), 6.084 (CPU) seconds, initialization time: 0.118 (wall), 0.040 (CPU) seconds.
[17:22:02] [map         ] Command(post): 
[17:22:02] [sort_prepare] Sorting...
[17:22:06] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 225)... 
[17:22:12] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
771,32,32530,0,0,33333,0,0,0.960149439601,0.0231524578841,0.0452146375792

[17:22:12] [bwamem      ] 4c21a44c9042d3b44a6729ccaaa2740e (base: tests_base/base_mapping)
[17:22:12] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[17:22:12] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e/reads.fastq
[17:22:12] [init        ] Output:/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e/out_bwamem.sam
[17:22:12] [map         ] Command(pre): 
[17:22:12] [map         ] Base run time file not existing, performing base run
[17:22:13] [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
[17:22:15] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads.fastq  -t 4 > out_bwamem.sam
[17:22:15] [map         ]    Mapping 30.00MB to 5.00MB with bwamem...
[17:22:32] [map         ]    Took 16.149 (wall), 50.220 (CPU) seconds, initialization time: 0.074 (wall), 0.032 (CPU) seconds.
[17:22:32] [map         ] Command(post): 
[17:22:32] [sort_prepare] Sorting...
[17:22:36] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 225)... 
[17:22:46] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
32408,925,0,0,0,33333,0,0,0.972249722497,1.0,0.985929632954

[17:22:46] [bwasw       ] 4c21a44c9042d3b44a6729ccaaa2740e (base: tests_base/base_mapping)
[17:22:46] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[17:22:46] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e/reads.fastq
[17:22:46] [init        ] Output:/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e/out_bwasw.sam
[17:22:46] [map         ] Command(pre): 
[17:22:46] [map         ] Base run time file not existing, performing base run
[17:22:46] [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
[17:22:48] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads.fastq  -t 4 > out_bwasw.sam
[17:22:48] [map         ]    Mapping 30.00MB to 5.00MB with bwasw...
[17:23:21] [map         ]    Took 32.377 (wall), 65.608 (CPU) seconds, initialization time: 0.089 (wall), 0.036 (CPU) seconds.
[17:23:21] [map         ] Command(post): 
[17:23:22] [sort_prepare] Sorting...
[17:23:25] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 225)... 
[17:23:35] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
32372,961,0,0,6,33333,0,0,0.971169711697,1.0,0.985374020242

[17:23:36] [ngm         ] 4c21a44c9042d3b44a6729ccaaa2740e (base: tests_base/base_mapping)
[17:23:36] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[17:23:36] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e/reads.fastq
[17:23:36] [init        ] Output:/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e/out_ngm.sam
[17:23:36] [map         ] Command(pre): 
[17:23:36] [map         ] Base run time file not existing, performing base run
[17:23:36] [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
[17:24:17] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/E_coli.fasta -t 4 --qry reads.fastq  --no-progress
[17:24:17] [map         ]    Mapping 30.00MB to 5.00MB with ngm...
[17:24:33] [map         ]    Took 15.062 (wall), 35.308 (CPU) seconds, initialization time: 3.781 (wall), 4.140 (CPU) seconds.
[17:24:33] [map         ] Command(post): 
[17:24:33] [sort_prepare] Sorting...
[17:24:37] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 225)... 
[17:24:46] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
32428,905,0,0,0,33333,0,0,0.972849728497,1.0,0.986238043825