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 Accessionb705aa0185e37b61d45ed27cf2a0ba62
Report timestampThu Jul 6 20:50:08 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/b705aa0185e37b61d45ed27cf2a0ba62.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1499365780.831269
report: {name: b705aa0185e37b61d45ed27cf2a0ba62}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    b705aa0185e37b61d45ed27cf2a0ba62: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 150,
      insert_size_error: 50, mutation_indel_avg_len: 1.0, mutation_indel_frac: 0.3,
      mutation_rate: 0.001, paired: true, 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
[20:29:46] [Main        ] framework cmd:  ./teaser.py setups_generated/b705aa0185e37b61d45ed27cf2a0ba62.yaml -mcpu
[20:29:46] [Main        ] framework hash: vevev
[20:29:46] [Main        ] deployment mode: devel (True)
[20:29:46] [Main        ] Test Runner Setup - ""

[20:29:46] [Main        ] Using Teaser for data set creation
[20:29:46] [Teaser      ] Init. Creating 1 test datasets.
[20:29:46] [Teaser      ] 
[20:29:46] [Teaser      ] Creating test b705aa0185e37b61d45ed27cf2a0ba62
[20:29:47] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62
[20:29:47] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62
[20:29:47] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[20:29:47] [Teaser      ] csample /project/teaser/genometeaser/references/D_melanogaster.fasta 2000 0.250000
[20:29:47] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[20:29:47] [Teaser      ] Sampling as contig: 17965 regions of size 2000 (pad 400), totalling 35931498 base pairs
[20:29:47] [Teaser      ] Sampling 17965 regions
[20:30:04] [Teaser      ] 10%
[20:30:07] [Teaser      ] 20%
[20:30:09] [Teaser      ] 30%
[20:30:11] [Teaser      ] 40%
[20:30:13] [Teaser      ] 50%
[20:30:16] [Teaser      ] 60%
[20:30:18] [Teaser      ] 70%
[20:30:21] [Teaser      ] 80%
[20:30:23] [Teaser      ] 90%
[20:30:26] [Teaser      ] 100%
[20:30:30] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62
[20:30:30] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 299429 --mp  --ll 150 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.2000.400.fasta
[20:30:30] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 299429 --mp  --ll 150 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.2000.400.fasta
[20:33:34] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.2000.400.fasta_1.fastq -> ./reads1.fastq
[20:33:34] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.2000.400.fasta_2.fastq -> ./reads2.fastq
[20:33:34] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.2000.400.fasta.fastq.sam -> ./mapping_comparison.sam
[20:33:34] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62
[20:33:34] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[20:33:34] [Teaser      ] Translating SAM file coordinates (as contig)...
[20:33:34] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[20:34:23] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.2000.400.fasta
[20:34:23] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.2000.400.fasta.index
[20:34:23] [Teaser      ] remove mapping_comparison_unfixed.sam
[20:34:23] [Teaser      ] Took 276 seconds for generating b705aa0185e37b61d45ed27cf2a0ba62
[20:34:23] [Main        ] Data set creation completed
[20:34:23] [Main        ] 
[20:34:25] [bowtie2     ] b705aa0185e37b61d45ed27cf2a0ba62 (base: tests_base/base_mapping)
[20:34:25] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[20:34:25] [init        ] Reads: /project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62/reads1.fastq
[20:34:25] [init        ] Output:/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62/out_bowtie2.sam
[20:34:25] [map         ] Command(pre): 
[20:34:25] [map         ] Base run time file not existing, performing base run
[20:34:25] [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
[20:34:48] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
[20:34:48] [map         ]    Mapping 83.00MB to 146.00MB with bowtie2...
[20:35:53] [map         ]    Took 64.320 (wall), 220.804 (CPU) seconds, initialization time: 4.682 (wall), 4.632 (CPU) seconds.
[20:35:53] [map         ] Command(post): 
[20:35:53] [sort_prepare] Sorting...
[20:36:48] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[20:37:20] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
545068,53429,361,0,0,598858,0,0,0.910728040408,0.999338135669,0.95297772758

[20:37:20] [bwa         ] b705aa0185e37b61d45ed27cf2a0ba62 (base: tests_base/base_mapping)
[20:37:20] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[20:37:20] [init        ] Reads: /project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62/reads1.fastq
[20:37:20] [init        ] Output:/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62/out_bwa.sam
[20:37:20] [map         ] Command(pre): 
[20:37:20] [map         ] Base run time file not existing, performing base run
[20:37:20] [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
[20:37:56] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq  -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads2.fastq  -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
[20:37:56] [map         ]    Mapping 83.00MB to 146.00MB with bwa...
[20:39:50] [map         ]    Took 113.998 (wall), 202.188 (CPU) seconds, initialization time: 9.390 (wall), 9.132 (CPU) seconds.
[20:39:50] [map         ] Command(post): 
[20:39:50] [sort_prepare] Sorting...
[20:40:16] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[20:41:17] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
545068,52700,1090,0,0,598858,0,0,0.911838706655,0.998004240531,0.95297772758

[20:41:18] [bwamem      ] b705aa0185e37b61d45ed27cf2a0ba62 (base: tests_base/base_mapping)
[20:41:18] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[20:41:18] [init        ] Reads: /project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62/reads1.fastq
[20:41:18] [init        ] Output:/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62/out_bwamem.sam
[20:41:18] [map         ] Command(pre): 
[20:41:18] [map         ] Base run time file not existing, performing base run
[20:41:18] [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
[20:41:26] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq  -t 4 > out_bwamem.sam
[20:41:26] [map         ]    Mapping 83.00MB to 146.00MB with bwamem...
[20:42:13] [map         ]    Took 46.972 (wall), 130.220 (CPU) seconds, initialization time: 2.661 (wall), 2.564 (CPU) seconds.
[20:42:13] [map         ] Command(post): 
[20:42:13] [sort_prepare] Sorting...
[20:42:31] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[20:43:00] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
545630,53228,0,0,0,598858,0,0,0.91111749363,1.0,0.953491867106

[20:43:00] [bwasw       ] b705aa0185e37b61d45ed27cf2a0ba62 (base: tests_base/base_mapping)
[20:43:00] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[20:43:00] [init        ] Reads: /project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62/reads1.fastq
[20:43:00] [init        ] Output:/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62/out_bwasw.sam
[20:43:00] [map         ] Command(pre): 
[20:43:01] [map         ] Base run time file not existing, performing base run
[20:43:01] [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
[20:43:06] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq  -t 4 > out_bwasw.sam
[20:43:06] [map         ]    Mapping 83.00MB to 146.00MB with bwasw...
[20:45:13] [map         ]    Took 126.309 (wall), 377.892 (CPU) seconds, initialization time: 2.276 (wall), 2.188 (CPU) seconds.
[20:45:13] [map         ] Command(post): 
[20:45:13] [sort_prepare] Sorting...
[20:45:35] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[20:46:33] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
536763,61507,588,0,29,598858,0,0,0.897191903321,0.998905743173,0.945320665962

[20:46:33] [ngm         ] b705aa0185e37b61d45ed27cf2a0ba62 (base: tests_base/base_mapping)
[20:46:33] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[20:46:33] [init        ] Reads: /project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62/reads1.fastq
[20:46:33] [init        ] Output:/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62/out_ngm.sam
[20:46:33] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/D_melanogaster.fasta 
[20:47:29] [map         ] Base run time file not existing, performing base run
[20:47:29] [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
[20:47:59] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4  --no-progress
[20:47:59] [map         ]    Mapping 83.00MB to 146.00MB with ngm...
[20:48:47] [map         ]    Took 47.019 (wall), 91.128 (CPU) seconds, initialization time: 12.269 (wall), 19.832 (CPU) seconds.
[20:48:47] [map         ] Command(post): 
[20:48:47] [sort_prepare] Sorting...
[20:49:09] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[20:50:08] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
543951,54556,351,0,0,598858,0,0,0.908846513073,0.999355137405,0.951954351077