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 Accessiond355779ac9fa0c29904cf2683bc616bd
Report timestampMon Oct 8 18:30:15 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/d355779ac9fa0c29904cf2683bc616bd.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 20}
include: [base_teaser.yaml]
meta_timestamp: 1539013406.632128
report: {name: d355779ac9fa0c29904cf2683bc616bd}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    d355779ac9fa0c29904cf2683bc616bd: {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: 40, 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
[17:43:28] [Main        ] framework cmd:  ./teaser.py setups_generated/d355779ac9fa0c29904cf2683bc616bd.yaml -mcpu
[17:43:28] [Main        ] framework hash: vevev
[17:43:28] [Main        ] deployment mode: devel (True)
[17:43:28] [Main        ] Test Runner Setup - ""

[17:43:28] [Main        ] Using Teaser for data set creation
[17:43:29] [Teaser      ] Init. Creating 1 test datasets.
[17:43:29] [Teaser      ] 
[17:43:29] [Teaser      ] Creating test d355779ac9fa0c29904cf2683bc616bd
[17:43:29] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd
[17:43:29] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd
[17:43:29] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[17:43:29] [Teaser      ] csample /project/teaser/genometeaser/references/H_sapiens.fa 400 0.010000
[17:43:29] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[17:43:29] [Teaser      ] Sampling as contig: 78429 regions of size 400 (pad 80), totalling 31371612 base pairs
[17:43:29] [Teaser      ] Sampling 78429 regions
[17:48:57] [Teaser      ] 10%
[17:49:18] [Teaser      ] 20%
[17:49:27] [Teaser      ] 30%
[17:49:36] [Teaser      ] 40%
[17:49:45] [Teaser      ] 50%
[17:49:54] [Teaser      ] 60%
[17:50:03] [Teaser      ] 70%
[17:50:12] [Teaser      ] 80%
[17:50:22] [Teaser      ] 90%
[17:50:31] [Teaser      ] 100%
[17:50:34] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd
[17:50:34] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 40 -N 784290  --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.100.400.80.fasta
[17:50:34] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 40 -N 784290  --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.100.400.80.fasta
[17:52:40] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.400.80.fasta.fastq -> ./reads.fastq
[17:52:40] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.400.80.fasta.fastq.sam -> ./mapping_comparison.sam
[17:52:40] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd
[17:52:40] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[17:52:40] [Teaser      ] Translating SAM file coordinates (as contig)...
[17:52:40] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[17:54:40] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.400.80.fasta
[17:54:40] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.400.80.fasta.index
[17:54:40] [Teaser      ] remove mapping_comparison_unfixed.sam
[17:54:40] [Teaser      ] Took 671 seconds for generating d355779ac9fa0c29904cf2683bc616bd
[17:54:40] [Main        ] Data set creation completed
[17:54:40] [Main        ] 
[17:54:42] [bowtie2     ] d355779ac9fa0c29904cf2683bc616bd (base: tests_base/base_mapping)
[17:54:42] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[17:54:42] [init        ] Reads: /project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd/reads.fastq
[17:54:42] [init        ] Output:/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd/out_bowtie2.sam
[17:54:42] [map         ] Command(pre): 
[17:54:42] [map         ] Base run time file not existing, performing base run
[17:54:42] [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
[17:59:37] [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
[17:59:37] [map         ]    Mapping 78.00MB to 3199.00MB with bowtie2...
[18:00:19] [map         ]    Took 41.187 (wall), 103.944 (CPU) seconds, initialization time: 3.726 (wall), 3.748 (CPU) seconds.
[18:00:19] [map         ] Command(post): 
[18:00:19] [sort_prepare] Sorting...
[18:01:13] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[18:02:18] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
687475,80972,15843,0,0,784290,3,0,0.894629037526,0.977473916493,0.934218438406

[18:02:18] [bwa         ] d355779ac9fa0c29904cf2683bc616bd (base: tests_base/base_mapping)
[18:02:18] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:02:18] [init        ] Reads: /project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd/reads.fastq
[18:02:18] [init        ] Output:/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd/out_bwa.sam
[18:02:18] [map         ] Command(pre): 
[18:02:19] [map         ] Base run time file not existing, performing base run
[18:02:19] [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
[18:10:17] [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
[18:10:17] [map         ]    Mapping 78.00MB to 3199.00MB with bwa...
[18:12:09] [map         ]    Took 111.430 (wall), 238.180 (CPU) seconds, initialization time: 7.284 (wall), 7.076 (CPU) seconds.
[18:12:10] [map         ] Command(post): 
[18:12:10] [sort_prepare] Sorting...
[18:12:31] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[18:13:35] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
697742,82314,4234,0,0,784290,3,0,0.894476806793,0.993968454762,0.941601800771

[18:13:35] [bwamem      ] d355779ac9fa0c29904cf2683bc616bd (base: tests_base/base_mapping)
[18:13:35] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:13:35] [init        ] Reads: /project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd/reads.fastq
[18:13:35] [init        ] Output:/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd/out_bwamem.sam
[18:13:35] [map         ] Command(pre): 
[18:13:35] [map         ] Base run time file not existing, performing base run
[18:13:35] [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
[18:13:45] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq  -t 4 > out_bwamem.sam
[18:13:45] [map         ]    Mapping 78.00MB to 3199.00MB with bwamem...
[18:14:57] [map         ]    Took 71.646 (wall), 221.212 (CPU) seconds, initialization time: 4.419 (wall), 4.348 (CPU) seconds.
[18:14:57] [map         ] Command(post): 
[18:14:57] [sort_prepare] Sorting...
[18:15:17] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[18:16:19] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
693365,81573,9352,0,0,784290,4,0,0.894736095017,0.986691655389,0.938466692158

[18:16:19] [bwasw       ] d355779ac9fa0c29904cf2683bc616bd (base: tests_base/base_mapping)
[18:16:19] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:16:19] [init        ] Reads: /project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd/reads.fastq
[18:16:19] [init        ] Output:/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd/out_bwasw.sam
[18:16:19] [map         ] Command(pre): 
[18:16:20] [map         ] Base run time file not existing, performing base run
[18:16:20] [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
[18:16:30] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq  -t 4 > out_bwasw.sam
[18:16:30] [map         ]    Mapping 78.00MB to 3199.00MB with bwasw...
[18:18:08] [map         ]    Took 97.887 (wall), 213.868 (CPU) seconds, initialization time: 4.512 (wall), 4.452 (CPU) seconds.
[18:18:08] [map         ] Command(post): 
[18:18:08] [sort_prepare] Sorting...
[18:18:27] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[18:19:27] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
586933,74806,122551,0,0,784290,3,0,0.886955431069,0.827267422521,0.856072280001

[18:19:27] [ngm         ] d355779ac9fa0c29904cf2683bc616bd (base: tests_base/base_mapping)
[18:19:27] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:19:27] [init        ] Reads: /project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd/reads.fastq
[18:19:27] [init        ] Output:/project/teaser/genometeaser/tests_generated/d355779ac9fa0c29904cf2683bc616bd/out_ngm.sam
[18:19:27] [map         ] Command(pre): 
[18:19:27] [map         ] Base run time file not existing, performing base run
[18:19:27] [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
[18:27:54] [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
[18:27:54] [map         ]    Mapping 78.00MB to 3199.00MB with ngm...
[18:28:49] [map         ]    Took 54.633 (wall), 141.188 (CPU) seconds, initialization time: 8.474 (wall), 8.648 (CPU) seconds.
[18:28:49] [map         ] Command(post): 
[18:28:49] [sort_prepare] Sorting...
[18:29:12] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[18:30:15] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
691180,72424,20686,0,0,784290,2,0,0.905155027999,0.970941160275,0.936894684406