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
Arabidopsis_thalianaArabidopsis_thaliana5500
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 Accessione1bc1c1fdc90a514d252971342a91347
Report timestampTue Jul 24 17:38:26 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/e1bc1c1fdc90a514d252971342a91347.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 75}
include: [base_teaser.yaml]
meta_timestamp: 1532445984.989567
report: {name: e1bc1c1fdc90a514d252971342a91347}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    e1bc1c1fdc90a514d252971342a91347: {coverage: 1.0, error_rate_mult: 1.0, mutation_indel_avg_len: 1.0,
      mutation_indel_frac: 0.0, mutation_rate: 0.0, paired: false, 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, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[17:26:26] [Main        ] framework cmd:  ./teaser.py setups_generated/e1bc1c1fdc90a514d252971342a91347.yaml -mcpu
[17:26:26] [Main        ] framework hash: vevev
[17:26:26] [Main        ] deployment mode: devel (True)
[17:26:26] [Main        ] Test Runner Setup - ""

[17:26:26] [Main        ] Using Teaser for data set creation
[17:26:27] [Teaser      ] Init. Creating 1 test datasets.
[17:26:27] [Teaser      ] 
[17:26:27] [Teaser      ] Creating test e1bc1c1fdc90a514d252971342a91347
[17:26:27] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347
[17:26:27] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347
[17:26:27] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.teaser.findex
[17:26:27] [Teaser      ] csample /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 1500 0.250000
[17:26:27] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.teaser.findex
[17:26:27] [Teaser      ] Sampling as contig: 19944 regions of size 1500 (pad 300), totalling 29916937 base pairs
[17:26:27] [Teaser      ] Sampling 19944 regions
[17:26:39] [Teaser      ] 10%
[17:26:41] [Teaser      ] 20%
[17:26:43] [Teaser      ] 30%
[17:26:45] [Teaser      ] 40%
[17:26:47] [Teaser      ] 50%
[17:26:49] [Teaser      ] 60%
[17:26:51] [Teaser      ] 70%
[17:26:53] [Teaser      ] 80%
[17:26:55] [Teaser      ] 90%
[17:26:57] [Teaser      ] 100%
[17:27:00] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347
[17:27:00] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 199446  --ll 500 --le 50  --hi 0.000000  --hs 0.000000  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.1500.300.fasta
[17:27:00] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 199446  --ll 500 --le 50  --hi 0.000000  --hs 0.000000  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.1500.300.fasta
[17:30:16] [Teaser      ] move /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.1500.300.fasta.fastq -> ./reads.fastq
[17:30:16] [Teaser      ] move /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.1500.300.fasta.fastq.sam -> ./mapping_comparison.sam
[17:30:16] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347
[17:30:16] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[17:30:16] [Teaser      ] Translating SAM file coordinates (as contig)...
[17:30:16] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.teaser.findex
[17:30:53] [Teaser      ] remove /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.1500.300.fasta
[17:30:53] [Teaser      ] remove /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.1500.300.fasta.index
[17:30:53] [Teaser      ] remove mapping_comparison_unfixed.sam
[17:30:53] [Teaser      ] Took 266 seconds for generating e1bc1c1fdc90a514d252971342a91347
[17:30:53] [Main        ] Data set creation completed
[17:30:53] [Main        ] 
[17:30:54] [bowtie2     ] e1bc1c1fdc90a514d252971342a91347 (base: tests_base/base_mapping)
[17:30:54] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[17:30:54] [init        ] Reads: /project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347/reads.fastq
[17:30:54] [init        ] Output:/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347/out_bowtie2.sam
[17:30:54] [map         ] Command(pre): 
[17:30:54] [map         ] Base run time file not existing, performing base run
[17:30:54] [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
[17:31:09] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads.fastq -S out_bowtie2.sam
[17:31:09] [map         ]    Mapping 63.00MB to 121.00MB with bowtie2...
[17:31:29] [map         ]    Took 19.340 (wall), 47.868 (CPU) seconds, initialization time: 0.523 (wall), 0.540 (CPU) seconds.
[17:31:29] [map         ] Command(post): 
[17:31:29] [sort_prepare] Sorting...
[17:31:52] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[17:32:13] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
196238,3208,0,0,0,199446,0,0,0.983915445785,1.0,0.991892520294

[17:32:13] [bwa         ] e1bc1c1fdc90a514d252971342a91347 (base: tests_base/base_mapping)
[17:32:13] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[17:32:13] [init        ] Reads: /project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347/reads.fastq
[17:32:13] [init        ] Output:/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347/out_bwa.sam
[17:32:13] [map         ] Command(pre): 
[17:32:13] [map         ] Base run time file not existing, performing base run
[17:32:13] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[17:32:33] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads.fastq > out_bwa.sam
[17:32:33] [map         ]    Mapping 63.00MB to 121.00MB with bwa...
[17:33:21] [map         ]    Took 46.654 (wall), 75.692 (CPU) seconds, initialization time: 0.415 (wall), 0.336 (CPU) seconds.
[17:33:21] [map         ] Command(post): 
[17:33:21] [sort_prepare] Sorting...
[17:33:30] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[17:33:50] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
190484,3123,5839,0,0,199446,0,0,0.983869384888,0.970258196951,0.977016387557

[17:33:50] [bwamem      ] e1bc1c1fdc90a514d252971342a91347 (base: tests_base/base_mapping)
[17:33:50] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[17:33:50] [init        ] Reads: /project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347/reads.fastq
[17:33:50] [init        ] Output:/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347/out_bwamem.sam
[17:33:50] [map         ] Command(pre): 
[17:33:50] [map         ] Base run time file not existing, performing base run
[17:33:51] [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
[17:33:53] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq  -t 4 > out_bwamem.sam
[17:33:53] [map         ]    Mapping 63.00MB to 121.00MB with bwamem...
[17:34:11] [map         ]    Took 16.982 (wall), 38.804 (CPU) seconds, initialization time: 0.260 (wall), 0.216 (CPU) seconds.
[17:34:11] [map         ] Command(post): 
[17:34:11] [sort_prepare] Sorting...
[17:34:19] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[17:34:40] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
196228,3218,0,0,0,199446,0,0,0.9838653069,1.0,0.99186704206

[17:34:40] [bwasw       ] e1bc1c1fdc90a514d252971342a91347 (base: tests_base/base_mapping)
[17:34:40] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[17:34:40] [init        ] Reads: /project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347/reads.fastq
[17:34:40] [init        ] Output:/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347/out_bwasw.sam
[17:34:40] [map         ] Command(pre): 
[17:34:40] [map         ] Base run time file not existing, performing base run
[17:34:40] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq  -t 4 > out_bwasw.sam
[17:34:42] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq  -t 4 > out_bwasw.sam
[17:34:42] [map         ]    Mapping 63.00MB to 121.00MB with bwasw...
[17:36:07] [map         ]    Took 84.389 (wall), 230.816 (CPU) seconds, initialization time: 0.270 (wall), 0.216 (CPU) seconds.
[17:36:07] [map         ] Command(post): 
[17:36:07] [sort_prepare] Sorting...
[17:36:16] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[17:36:36] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
196131,3314,1,0,1,199446,0,0,0.983383890296,0.999994901393,0.99161983634

[17:36:36] [ngm         ] e1bc1c1fdc90a514d252971342a91347 (base: tests_base/base_mapping)
[17:36:36] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[17:36:36] [init        ] Reads: /project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347/reads.fastq
[17:36:36] [init        ] Output:/project/teaser/genometeaser/tests_generated/e1bc1c1fdc90a514d252971342a91347/out_ngm.sam
[17:36:36] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 
[17:37:25] [map         ] Base run time file not existing, performing base run
[17:37:25] [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
[17:37:32] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas -t 4 --qry reads.fastq  --no-progress
[17:37:32] [map         ]    Mapping 63.00MB to 121.00MB with ngm...
[17:37:56] [map         ]    Took 23.497 (wall), 49.768 (CPU) seconds, initialization time: 3.196 (wall), 3.468 (CPU) seconds.
[17:37:56] [map         ] Command(post): 
[17:37:56] [sort_prepare] Sorting...
[17:38:06] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[17:38:26] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
196008,3438,0,0,0,199446,0,0,0.982762251436,1.0,0.991306194905