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
H_sapiensH_sapiens5500
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 Accession73b7a31da9ec873be5a7818478a53cf8
Report timestampMon Oct 8 13:55:40 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/73b7a31da9ec873be5a7818478a53cf8.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1538997153.649529
report: {name: 73b7a31da9ec873be5a7818478a53cf8}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    73b7a31da9ec873be5a7818478a53cf8: {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: 60, reference: !!python/unicode 'H_sapiens.fa', title: !!python/unicode 'H_sapiens',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[13:12:35] [Main        ] framework cmd:  ./teaser.py setups_generated/73b7a31da9ec873be5a7818478a53cf8.yaml -mcpu
[13:12:35] [Main        ] framework hash: vevev
[13:12:35] [Main        ] deployment mode: devel (True)
[13:12:35] [Main        ] Test Runner Setup - ""

[13:12:36] [Main        ] Using Teaser for data set creation
[13:12:36] [Teaser      ] Init. Creating 1 test datasets.
[13:12:36] [Teaser      ] 
[13:12:36] [Teaser      ] Creating test 73b7a31da9ec873be5a7818478a53cf8
[13:12:36] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8
[13:12:36] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8
[13:12:36] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[13:12:36] [Teaser      ] csample /project/teaser/genometeaser/references/H_sapiens.fa 600 0.010000
[13:12:36] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[13:12:36] [Teaser      ] Sampling as contig: 52286 regions of size 600 (pad 120), totalling 31371612 base pairs
[13:12:36] [Teaser      ] Sampling 52286 regions
[13:17:33] [Teaser      ] 10%
[13:18:11] [Teaser      ] 20%
[13:18:22] [Teaser      ] 30%
[13:18:29] [Teaser      ] 40%
[13:18:35] [Teaser      ] 50%
[13:18:41] [Teaser      ] 60%
[13:18:47] [Teaser      ] 70%
[13:18:53] [Teaser      ] 80%
[13:18:59] [Teaser      ] 90%
[13:19:05] [Teaser      ] 100%
[13:19:08] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8
[13:19:08] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 522860  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.600.120.fasta
[13:19:08] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 522860  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.600.120.fasta
[13:21:21] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.600.120.fasta.fastq -> ./reads.fastq
[13:21:21] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.600.120.fasta.fastq.sam -> ./mapping_comparison.sam
[13:21:21] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8
[13:21:21] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[13:21:21] [Teaser      ] Translating SAM file coordinates (as contig)...
[13:21:21] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[13:22:42] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.600.120.fasta
[13:22:42] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.600.120.fasta.index
[13:22:42] [Teaser      ] remove mapping_comparison_unfixed.sam
[13:22:42] [Teaser      ] Took 606 seconds for generating 73b7a31da9ec873be5a7818478a53cf8
[13:22:42] [Main        ] Data set creation completed
[13:22:42] [Main        ] 
[13:22:44] [bowtie2     ] 73b7a31da9ec873be5a7818478a53cf8 (base: tests_base/base_mapping)
[13:22:45] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[13:22:45] [init        ] Reads: /project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8/reads.fastq
[13:22:45] [init        ] Output:/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8/out_bowtie2.sam
[13:22:45] [map         ] Command(pre): 
[13:22:45] [map         ] Base run time file not existing, performing base run
[13:22:45] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
[13:27:39] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads.fastq -S out_bowtie2.sam
[13:27:39] [map         ]    Mapping 73.00MB to 3199.00MB with bowtie2...
[13:28:25] [map         ]    Took 45.212 (wall), 152.944 (CPU) seconds, initialization time: 3.756 (wall), 3.736 (CPU) seconds.
[13:28:25] [map         ] Command(post): 
[13:28:26] [sort_prepare] Sorting...
[13:29:11] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[13:29:58] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
488229,32497,2134,0,0,522860,0,0,0.937592899145,0.995648121902,0.96574881143

[13:29:58] [bwa         ] 73b7a31da9ec873be5a7818478a53cf8 (base: tests_base/base_mapping)
[13:29:58] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[13:29:58] [init        ] Reads: /project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8/reads.fastq
[13:29:58] [init        ] Output:/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8/out_bwa.sam
[13:29:58] [map         ] Command(pre): 
[13:29:58] [map         ] Base run time file not existing, performing base run
[13:29:58] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[13:37:57] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads.fastq > out_bwa.sam
[13:37:57] [map         ]    Mapping 73.00MB to 3199.00MB with bwa...
[13:39:34] [map         ]    Took 96.504 (wall), 206.752 (CPU) seconds, initialization time: 7.243 (wall), 7.112 (CPU) seconds.
[13:39:34] [map         ] Command(post): 
[13:39:34] [sort_prepare] Sorting...
[13:39:52] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[13:40:38] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
486413,31171,5276,0,0,522860,0,0,0.939775959071,0.989269639955,0.963887867802

[13:40:38] [bwamem      ] 73b7a31da9ec873be5a7818478a53cf8 (base: tests_base/base_mapping)
[13:40:38] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[13:40:38] [init        ] Reads: /project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8/reads.fastq
[13:40:38] [init        ] Output:/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8/out_bwamem.sam
[13:40:38] [map         ] Command(pre): 
[13:40:38] [map         ] Base run time file not existing, performing base run
[13:40:38] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -t 4 > out_bwamem.sam
[13:40:48] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq  -t 4 > out_bwamem.sam
[13:40:48] [map         ]    Mapping 73.00MB to 3199.00MB with bwamem...
[13:41:38] [map         ]    Took 49.693 (wall), 144.112 (CPU) seconds, initialization time: 4.503 (wall), 4.440 (CPU) seconds.
[13:41:38] [map         ] Command(post): 
[13:41:38] [sort_prepare] Sorting...
[13:41:52] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[13:42:37] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
491495,31277,88,0,0,522860,1,1,0.940170858424,0.999820986487,0.969078872781

[13:42:37] [bwasw       ] 73b7a31da9ec873be5a7818478a53cf8 (base: tests_base/base_mapping)
[13:42:37] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[13:42:37] [init        ] Reads: /project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8/reads.fastq
[13:42:37] [init        ] Output:/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8/out_bwasw.sam
[13:42:37] [map         ] Command(pre): 
[13:42:37] [map         ] Base run time file not existing, performing base run
[13:42:37] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -t 4 > out_bwasw.sam
[13:42:48] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq  -t 4 > out_bwasw.sam
[13:42:48] [map         ]    Mapping 73.00MB to 3199.00MB with bwasw...
[13:44:19] [map         ]    Took 90.495 (wall), 220.240 (CPU) seconds, initialization time: 4.539 (wall), 4.452 (CPU) seconds.
[13:44:19] [map         ] Command(post): 
[13:44:19] [sort_prepare] Sorting...
[13:44:36] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[13:45:21] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
470625,32390,19845,0,46,522860,0,0,0.935608282059,0.959538809713,0.947422457309

[13:45:21] [ngm         ] 73b7a31da9ec873be5a7818478a53cf8 (base: tests_base/base_mapping)
[13:45:21] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[13:45:21] [init        ] Reads: /project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8/reads.fastq
[13:45:21] [init        ] Output:/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8/out_ngm.sam
[13:45:21] [map         ] Command(pre): 
[13:45:21] [map         ] Base run time file not existing, performing base run
[13:45:21] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq  --no-progress
[13:53:48] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads.fastq  --no-progress
[13:53:48] [map         ]    Mapping 73.00MB to 3199.00MB with ngm...
[13:54:37] [map         ]    Took 48.932 (wall), 129.128 (CPU) seconds, initialization time: 8.548 (wall), 8.580 (CPU) seconds.
[13:54:37] [map         ] Command(post): 
[13:54:37] [sort_prepare] Sorting...
[13:54:53] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[13:55:39] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
482789,33883,6188,0,0,522860,0,0,0.934420676948,0.987345008047,0.960154089548