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.

4 tests executed, 0 fail, 0 aborted, 0 errors total.
StateNameReferenceExecutedOKWarningsErrors
Arabidopsis_thalianaArabidopsis_thaliana4400
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 Accessionff62cbf4348f21949b4a4be50bea9679
Report timestampMon Aug 27 03:41:17 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/ff62cbf4348f21949b4a4be50bea9679.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 75}
include: [base_teaser.yaml]
meta_timestamp: 1535332375.515199
report: {name: ff62cbf4348f21949b4a4be50bea9679}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    ff62cbf4348f21949b4a4be50bea9679: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 350,
      insert_size_error: 148, mutation_indel_avg_len: 2.0, mutation_indel_frac: 0.3,
      mutation_rate: 0.05, paired: true, platform: !!python/unicode 'illumina', read_length: 150,
      reference: !!python/unicode 'Arabidopsis_thaliana.fas', title: !!python/unicode 'Arabidopsis_thaliana',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwamem, ngm, stampy]
test_parameters: []
threads: 4
Log
[03:12:57] [Main        ] framework cmd:  ./teaser.py setups_generated/ff62cbf4348f21949b4a4be50bea9679.yaml -mcpu
[03:12:57] [Main        ] framework hash: vevev
[03:12:57] [Main        ] deployment mode: devel (True)
[03:12:57] [Main        ] Test Runner Setup - ""

[03:12:57] [Main        ] Using Teaser for data set creation
[03:12:58] [Teaser      ] Init. Creating 1 test datasets.
[03:12:58] [Teaser      ] 
[03:12:58] [Teaser      ] Creating test ff62cbf4348f21949b4a4be50bea9679
[03:12:58] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679
[03:12:58] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679
[03:12:58] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.teaser.findex
[03:12:58] [Teaser      ] csample /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 4980 0.250000
[03:12:58] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.teaser.findex
[03:12:58] [Teaser      ] Sampling as contig: 6007 regions of size 4980 (pad 996), totalling 29916937 base pairs
[03:12:58] [Teaser      ] Sampling 6007 regions
[03:13:11] [Teaser      ] 10%
[03:13:12] [Teaser      ] 20%
[03:13:12] [Teaser      ] 30%
[03:13:13] [Teaser      ] 40%
[03:13:14] [Teaser      ] 50%
[03:13:14] [Teaser      ] 60%
[03:13:15] [Teaser      ] 70%
[03:13:15] [Teaser      ] 80%
[03:13:16] [Teaser      ] 90%
[03:13:17] [Teaser      ] 100%
[03:13:22] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679
[03:13:22] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 99723 --mp  --ll 350 --le 148  --hi 0.015000  --hs 0.035000  --hm 1 --hM 6 --source-no-N  /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4980.996.fasta
[03:13:22] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 99723 --mp  --ll 350 --le 148  --hi 0.015000  --hs 0.035000  --hm 1 --hM 6 --source-no-N  /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4980.996.fasta
[03:19:14] [Teaser      ] move /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4980.996.fasta_1.fastq -> ./reads1.fastq
[03:19:14] [Teaser      ] move /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4980.996.fasta_2.fastq -> ./reads2.fastq
[03:19:14] [Teaser      ] move /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4980.996.fasta.fastq.sam -> ./mapping_comparison.sam
[03:19:14] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679
[03:19:14] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[03:19:14] [Teaser      ] Translating SAM file coordinates (as contig)...
[03:19:14] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.teaser.findex
[03:19:48] [Teaser      ] remove /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4980.996.fasta
[03:19:48] [Teaser      ] remove /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4980.996.fasta.index
[03:19:48] [Teaser      ] remove mapping_comparison_unfixed.sam
[03:19:48] [Teaser      ] Took 410 seconds for generating ff62cbf4348f21949b4a4be50bea9679
[03:19:48] [Main        ] Data set creation completed
[03:19:48] [Main        ] 
[03:19:50] [bowtie2     ] ff62cbf4348f21949b4a4be50bea9679 (base: tests_base/base_mapping)
[03:19:51] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[03:19:51] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679/reads1.fastq
[03:19:51] [init        ] Output:/project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679/out_bowtie2.sam
[03:19:51] [map         ] Command(pre): 
[03:19:51] [map         ] Base run time file not existing, performing base run
[03:19:51] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam
[03:20:10] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
[03:20:10] [map         ]    Mapping 63.00MB to 121.00MB with bowtie2...
[03:20:59] [map         ]    Took 48.385 (wall), 139.528 (CPU) seconds, initialization time: 3.546 (wall), 3.612 (CPU) seconds.
[03:20:59] [map         ] Command(post): 
[03:20:59] [sort_prepare] Sorting...
[03:21:29] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[03:22:06] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
176854,2528,20064,0,0,199446,0,0,0.985907170173,0.898109873145,0.939962795642

[03:22:06] [bwamem      ] ff62cbf4348f21949b4a4be50bea9679 (base: tests_base/base_mapping)
[03:22:06] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[03:22:06] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679/reads1.fastq
[03:22:06] [init        ] Output:/project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679/out_bwamem.sam
[03:22:06] [map         ] Command(pre): 
[03:22:06] [map         ] Base run time file not existing, performing base run
[03:22:06] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq  -t 4 > out_bwamem.sam
[03:22:29] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq  -t 4 > out_bwamem.sam
[03:22:29] [map         ]    Mapping 63.00MB to 121.00MB with bwamem...
[03:23:15] [map         ]    Took 45.098 (wall), 105.204 (CPU) seconds, initialization time: 3.194 (wall), 3.120 (CPU) seconds.
[03:23:15] [map         ] Command(post): 
[03:23:15] [sort_prepare] Sorting...
[03:23:29] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[03:24:04] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
197156,2290,0,0,0,199446,0,1,0.988518195401,1.0,0.99422594944

[03:24:05] [ngm         ] ff62cbf4348f21949b4a4be50bea9679 (base: tests_base/base_mapping)
[03:24:05] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[03:24:05] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679/reads1.fastq
[03:24:05] [init        ] Output:/project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679/out_ngm.sam
[03:24:05] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 
[03:25:03] [map         ] Base run time file not existing, performing base run
[03:25:03] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas -t 4 --qry reads_base.fastq  --no-progress
[03:26:14] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas -t 4  --no-progress
[03:26:14] [map         ]    Mapping 63.00MB to 121.00MB with ngm...
[03:27:22] [map         ]    Took 67.472 (wall), 126.820 (CPU) seconds, initialization time: 32.628 (wall), 49.084 (CPU) seconds.
[03:27:22] [map         ] Command(post): 
[03:27:24] [sort_prepare] Sorting...
[03:27:40] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[03:28:16] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
197119,2305,22,0,0,199446,0,0,0.988441712131,0.999888404746,0.99413210949

[03:28:16] [stampy      ] ff62cbf4348f21949b4a4be50bea9679 (base: tests_base/base_mapping)
[03:28:16] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[03:28:16] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679/reads1.fastq
[03:28:16] [init        ] Output:/project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679/out_stampy.sam
[03:28:16] [map         ] Command(pre): /project/teaser/genometeaser/software/stampy -G /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas; /project/teaser/genometeaser/software/stampy -g /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -H /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o
[03:31:04] [map         ] Base run time file not existing, performing base run
[03:31:04] [map         ] Command(pre-b): /project/teaser/genometeaser/software/stampy  -t 4 -g /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -h /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -M reads_base.fastq -o out_stampy.sam
[03:31:09] [map         ] Command(main): /project/teaser/genometeaser/software/stampy  -t 4 -g /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -h /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -o out_stampy.sam -M reads1.fastq reads2.fastq
[03:31:09] [map         ]    Mapping 63.00MB to 121.00MB with stampy...
[03:40:28] [map         ]    Took 559.123 (wall), 2293.688 (CPU) seconds, initialization time: 0.621 (wall), 0.456 (CPU) seconds.
[03:40:28] [map         ] Command(post): 
[03:40:29] [sort_prepare] Sorting...
[03:40:42] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[03:41:17] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
197033,2413,0,0,0,199446,0,0,0.987901487119,1.0,0.993913927345