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 Accession58281c12b324089e734fe0553bf2f5c0
Report timestampWed Oct 3 17:04:25 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/58281c12b324089e734fe0553bf2f5c0.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1538577861.090541
report: {name: 58281c12b324089e734fe0553bf2f5c0}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    58281c12b324089e734fe0553bf2f5c0: {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
[16:45:20] [Main        ] framework cmd:  ./teaser.py setups_generated/58281c12b324089e734fe0553bf2f5c0.yaml -mcpu
[16:45:20] [Main        ] framework hash: vevev
[16:45:20] [Main        ] deployment mode: devel (True)
[16:45:20] [Main        ] Test Runner Setup - ""

[16:45:23] [Main        ] Using Teaser for data set creation
[16:45:41] [Teaser      ] Init. Creating 1 test datasets.
[16:45:41] [Teaser      ] 
[16:45:41] [Teaser      ] Creating test 58281c12b324089e734fe0553bf2f5c0
[16:45:41] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0
[16:45:41] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0
[16:45:42] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[16:45:42] [Teaser      ] csample /project/teaser/genometeaser/references/D_melanogaster.fasta 600 0.250000
[16:45:42] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[16:45:42] [Teaser      ] Sampling as contig: 59885 regions of size 600 (pad 120), totalling 35931498 base pairs
[16:45:42] [Teaser      ] Sampling 59885 regions
[16:45:53] [Teaser      ] 10%
[16:46:05] [Teaser      ] 20%
[16:46:17] [Teaser      ] 30%
[16:46:29] [Teaser      ] 40%
[16:46:42] [Teaser      ] 50%
[16:46:55] [Teaser      ] 60%
[16:47:08] [Teaser      ] 70%
[16:47:21] [Teaser      ] 80%
[16:47:35] [Teaser      ] 90%
[16:47:48] [Teaser      ] 100%
[16:47:53] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0
[16:47:54] [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
[16:47:54] [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
[16:50:29] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq -> ./reads.fastq
[16:50:29] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq.sam -> ./mapping_comparison.sam
[16:50:29] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0
[16:50:29] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[16:50:29] [Teaser      ] Translating SAM file coordinates (as contig)...
[16:50:29] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[16:52:00] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta
[16:52:00] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.index
[16:52:00] [Teaser      ] remove mapping_comparison_unfixed.sam
[16:52:00] [Teaser      ] Took 378 seconds for generating 58281c12b324089e734fe0553bf2f5c0
[16:52:00] [Main        ] Data set creation completed
[16:52:00] [Main        ] 
[16:52:06] [bowtie2     ] 58281c12b324089e734fe0553bf2f5c0 (base: tests_base/base_mapping)
[16:52:06] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[16:52:06] [init        ] Reads: /project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0/reads.fastq
[16:52:06] [init        ] Output:/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0/out_bowtie2.sam
[16:52:06] [map         ] Command(pre): 
[16:52:06] [map         ] Base run time file not existing, performing base run
[16:52:06] [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
[16:52:13] [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
[16:52:14] [map         ]    Mapping 83.00MB to 146.00MB with bowtie2...
[16:52:42] [map         ]    Took 27.135 (wall), 60.592 (CPU) seconds, initialization time: 0.529 (wall), 0.584 (CPU) seconds.
[16:52:42] [map         ] Command(post): 
[16:52:42] [sort_prepare] Sorting...
[16:53:29] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[16:54:22] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
527349,69625,1884,0,0,598858,0,0,0.883370130022,0.996440131284,0.936504567988

[16:54:22] [bwa         ] 58281c12b324089e734fe0553bf2f5c0 (base: tests_base/base_mapping)
[16:54:22] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[16:54:22] [init        ] Reads: /project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0/reads.fastq
[16:54:22] [init        ] Output:/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0/out_bwa.sam
[16:54:22] [map         ] Command(pre): 
[16:54:22] [map         ] Base run time file not existing, performing base run
[16:54:23] [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
[16:54:25] [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
[16:54:25] [map         ]    Mapping 83.00MB to 146.00MB with bwa...
[16:55:28] [map         ]    Took 62.082 (wall), 107.348 (CPU) seconds, initialization time: 0.511 (wall), 0.384 (CPU) seconds.
[16:55:28] [map         ] Command(post): 
[16:55:30] [sort_prepare] Sorting...
[16:55:56] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[16:56:50] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
523497,69161,6200,0,0,598858,0,0,0.883303692855,0.988295195178,0.932854578097

[16:56:55] [bwamem      ] 58281c12b324089e734fe0553bf2f5c0 (base: tests_base/base_mapping)
[16:56:58] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[16:56:58] [init        ] Reads: /project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0/reads.fastq
[16:56:58] [init        ] Output:/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0/out_bwamem.sam
[16:57:01] [map         ] Command(pre): 
[16:57:02] [map         ] Base run time file not existing, performing base run
[16:57:03] [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
[16:57:20] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwamem.sam
[16:57:20] [map         ]    Mapping 83.00MB to 146.00MB with bwamem...
[16:58:01] [map         ]    Took 39.457 (wall), 85.588 (CPU) seconds, initialization time: 4.287 (wall), 0.300 (CPU) seconds.
[16:58:01] [map         ] Command(post): 
[16:58:04] [sort_prepare] Sorting...
[16:58:24] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[16:59:18] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
529023,69748,87,0,0,598858,0,0,0.883514732677,0.999835572943,0.938083006984

[16:59:23] [bwasw       ] 58281c12b324089e734fe0553bf2f5c0 (base: tests_base/base_mapping)
[16:59:26] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[16:59:26] [init        ] Reads: /project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0/reads.fastq
[16:59:26] [init        ] Output:/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0/out_bwasw.sam
[16:59:28] [map         ] Command(pre): 
[16:59:30] [map         ] Base run time file not existing, performing base run
[16:59:30] [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
[16:59:49] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwasw.sam
[16:59:50] [map         ]    Mapping 83.00MB to 146.00MB with bwasw...
[17:01:25] [map         ]    Took 94.051 (wall), 215.460 (CPU) seconds, initialization time: 6.508 (wall), 0.296 (CPU) seconds.
[17:01:25] [map         ] Command(post): 
[17:01:28] [sort_prepare] Sorting...
[17:01:48] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[17:02:11] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
514278,69148,15432,0,20,598858,0,0,0.881479399273,0.970867078213,0.924016472381

[17:02:15] [ngm         ] 58281c12b324089e734fe0553bf2f5c0 (base: tests_base/base_mapping)
[17:02:17] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[17:02:17] [init        ] Reads: /project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0/reads.fastq
[17:02:17] [init        ] Output:/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0/out_ngm.sam
[17:02:20] [map         ] Command(pre): 
[17:02:21] [map         ] Base run time file not existing, performing base run
[17:02:22] [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
[17:02:55] [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
[17:02:55] [map         ]    Mapping 83.00MB to 146.00MB with ngm...
[17:03:33] [map         ]    Took 36.759 (wall), 59.412 (CPU) seconds, initialization time: 12.461 (wall), 3.652 (CPU) seconds.
[17:03:33] [map         ] Command(post): 
[17:03:34] [sort_prepare] Sorting...
[17:03:51] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[17:04:24] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
528371,69804,683,0,0,598858,0,0,0.883305052869,0.998709016471,0.937468784071