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
D_melanogasterD_melanogaster5500
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 Accession572b02d835a09aa985fb40e23486baf8
Report timestampWed Aug 2 18:18:52 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/572b02d835a09aa985fb40e23486baf8.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1501689895.581257
report: {name: 572b02d835a09aa985fb40e23486baf8}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    572b02d835a09aa985fb40e23486baf8: {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 'D_melanogaster.fasta', title: !!python/unicode 'D_melanogaster',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[18:04:59] [Main        ] framework cmd:  ./teaser.py setups_generated/572b02d835a09aa985fb40e23486baf8.yaml -mcpu
[18:04:59] [Main        ] framework hash: vevev
[18:04:59] [Main        ] deployment mode: devel (True)
[18:04:59] [Main        ] Test Runner Setup - ""

[18:04:59] [Main        ] Using Teaser for data set creation
[18:04:59] [Teaser      ] Init. Creating 1 test datasets.
[18:04:59] [Teaser      ] 
[18:04:59] [Teaser      ] Creating test 572b02d835a09aa985fb40e23486baf8
[18:04:59] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8
[18:04:59] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8
[18:04:59] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[18:04:59] [Teaser      ] csample /project/teaser/genometeaser/references/D_melanogaster.fasta 600 0.250000
[18:04:59] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[18:04:59] [Teaser      ] Sampling as contig: 59885 regions of size 600 (pad 120), totalling 35931498 base pairs
[18:04:59] [Teaser      ] Sampling 59885 regions
[18:05:20] [Teaser      ] 10%
[18:05:27] [Teaser      ] 20%
[18:05:34] [Teaser      ] 30%
[18:05:41] [Teaser      ] 40%
[18:05:49] [Teaser      ] 50%
[18:05:57] [Teaser      ] 60%
[18:06:05] [Teaser      ] 70%
[18:06:14] [Teaser      ] 80%
[18:06:22] [Teaser      ] 90%
[18:06:30] [Teaser      ] 100%
[18:06:32] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8
[18:06:32] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 598858  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta
[18:06:32] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 598858  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta
[18:07:59] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq -> ./reads.fastq
[18:07:59] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq.sam -> ./mapping_comparison.sam
[18:07:59] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8
[18:07:59] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[18:07:59] [Teaser      ] Translating SAM file coordinates (as contig)...
[18:07:59] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[18:08:50] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta
[18:08:50] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.index
[18:08:50] [Teaser      ] remove mapping_comparison_unfixed.sam
[18:08:50] [Teaser      ] Took 230 seconds for generating 572b02d835a09aa985fb40e23486baf8
[18:08:50] [Main        ] Data set creation completed
[18:08:50] [Main        ] 
[18:08:52] [bowtie2     ] 572b02d835a09aa985fb40e23486baf8 (base: tests_base/base_mapping)
[18:08:52] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[18:08:52] [init        ] Reads: /project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8/reads.fastq
[18:08:52] [init        ] Output:/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8/out_bowtie2.sam
[18:08:52] [map         ] Command(pre): 
[18:08:52] [map         ] Base run time file not existing, performing base run
[18:08:52] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
[18:09:10] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads.fastq -S out_bowtie2.sam
[18:09:10] [map         ]    Mapping 83.00MB to 146.00MB with bowtie2...
[18:09:43] [map         ]    Took 32.070 (wall), 80.488 (CPU) seconds, initialization time: 0.631 (wall), 0.636 (CPU) seconds.
[18:09:43] [map         ] Command(post): 
[18:09:43] [sort_prepare] Sorting...
[18:10:30] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[18:10:55] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
526604,70370,1884,0,0,598858,0,0,0.882122169475,0.996435113002,0.935800586781

[18:10:55] [bwa         ] 572b02d835a09aa985fb40e23486baf8 (base: tests_base/base_mapping)
[18:10:55] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[18:10:55] [init        ] Reads: /project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8/reads.fastq
[18:10:55] [init        ] Output:/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8/out_bwa.sam
[18:10:55] [map         ] Command(pre): 
[18:10:55] [map         ] Base run time file not existing, performing base run
[18:10:55] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[18:11:19] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
[18:11:19] [map         ]    Mapping 83.00MB to 146.00MB with bwa...
[18:12:20] [map         ]    Took 59.476 (wall), 123.392 (CPU) seconds, initialization time: 0.537 (wall), 0.452 (CPU) seconds.
[18:12:20] [map         ] Command(post): 
[18:12:20] [sort_prepare] Sorting...
[18:12:37] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[18:13:03] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
522885,69767,6206,0,0,598858,0,0,0.882279988931,0.988270448751,0.932272365417

[18:13:03] [bwamem      ] 572b02d835a09aa985fb40e23486baf8 (base: tests_base/base_mapping)
[18:13:03] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[18:13:03] [init        ] Reads: /project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8/reads.fastq
[18:13:03] [init        ] Output:/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8/out_bwamem.sam
[18:13:03] [map         ] Command(pre): 
[18:13:03] [map         ] Base run time file not existing, performing base run
[18:13:03] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq  -t 4 > out_bwamem.sam
[18:13:05] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwamem.sam
[18:13:05] [map         ]    Mapping 83.00MB to 146.00MB with bwamem...
[18:13:41] [map         ]    Took 35.587 (wall), 94.312 (CPU) seconds, initialization time: 0.353 (wall), 0.308 (CPU) seconds.
[18:13:41] [map         ] Command(post): 
[18:13:41] [sort_prepare] Sorting...
[18:14:01] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[18:14:25] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
528330,70435,93,0,0,598858,0,0,0.882366203769,0.999824004633,0.937430135878

[18:14:25] [bwasw       ] 572b02d835a09aa985fb40e23486baf8 (base: tests_base/base_mapping)
[18:14:25] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[18:14:25] [init        ] Reads: /project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8/reads.fastq
[18:14:25] [init        ] Output:/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8/out_bwasw.sam
[18:14:25] [map         ] Command(pre): 
[18:14:25] [map         ] Base run time file not existing, performing base run
[18:14:25] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq  -t 4 > out_bwasw.sam
[18:14:28] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwasw.sam
[18:14:28] [map         ]    Mapping 83.00MB to 146.00MB with bwasw...
[18:15:40] [map         ]    Took 71.204 (wall), 230.860 (CPU) seconds, initialization time: 0.372 (wall), 0.300 (CPU) seconds.
[18:15:40] [map         ] Command(post): 
[18:15:40] [sort_prepare] Sorting...
[18:15:55] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[18:16:19] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
513572,70025,15261,0,34,598858,0,0,0.880011377714,0.971142118589,0.923333603013

[18:16:19] [ngm         ] 572b02d835a09aa985fb40e23486baf8 (base: tests_base/base_mapping)
[18:16:19] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[18:16:19] [init        ] Reads: /project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8/reads.fastq
[18:16:19] [init        ] Output:/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8/out_ngm.sam
[18:16:19] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/D_melanogaster.fasta 
[18:17:12] [map         ] Base run time file not existing, performing base run
[18:17:12] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads_base.fastq  --no-progress
[18:17:34] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads.fastq  --no-progress
[18:17:34] [map         ]    Mapping 83.00MB to 146.00MB with ngm...
[18:18:08] [map         ]    Took 33.327 (wall), 64.288 (CPU) seconds, initialization time: 4.031 (wall), 4.820 (CPU) seconds.
[18:18:08] [map         ] Command(post): 
[18:18:08] [sort_prepare] Sorting...
[18:18:26] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[18:18:52] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
527988,70208,662,0,0,598858,0,0,0.882633785582,0.998747753712,0.937107643813