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 Accessionf2a6f25cabc55338e734f1adbe44516b
Report timestampWed Jul 5 23:59:52 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/f2a6f25cabc55338e734f1adbe44516b.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1499290230.44928
report: {name: f2a6f25cabc55338e734f1adbe44516b}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    f2a6f25cabc55338e734f1adbe44516b: {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
[23:30:34] [Main        ] framework cmd:  ./teaser.py setups_generated/f2a6f25cabc55338e734f1adbe44516b.yaml -mcpu
[23:30:34] [Main        ] framework hash: vevev
[23:30:34] [Main        ] deployment mode: devel (True)
[23:30:34] [Main        ] Test Runner Setup - ""

[23:30:34] [Main        ] Using Teaser for data set creation
[23:30:34] [Teaser      ] Init. Creating 1 test datasets.
[23:30:34] [Teaser      ] 
[23:30:34] [Teaser      ] Creating test f2a6f25cabc55338e734f1adbe44516b
[23:30:34] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b
[23:30:34] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b
[23:30:34] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[23:30:34] [Teaser      ] csample /project/teaser/genometeaser/references/D_melanogaster.fasta 600 0.250000
[23:30:34] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[23:30:34] [Teaser      ] Sampling as contig: 59885 regions of size 600 (pad 120), totalling 35931498 base pairs
[23:30:35] [Teaser      ] Sampling 59885 regions
[23:31:01] [Teaser      ] 10%
[23:31:15] [Teaser      ] 20%
[23:31:29] [Teaser      ] 30%
[23:31:43] [Teaser      ] 40%
[23:31:58] [Teaser      ] 50%
[23:32:13] [Teaser      ] 60%
[23:32:28] [Teaser      ] 70%
[23:32:43] [Teaser      ] 80%
[23:33:00] [Teaser      ] 90%
[23:33:15] [Teaser      ] 100%
[23:33:19] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b
[23:33:19] [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
[23:33:19] [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
[23:36:32] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq -> ./reads.fastq
[23:36:32] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq.sam -> ./mapping_comparison.sam
[23:36:32] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b
[23:36:32] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[23:36:32] [Teaser      ] Translating SAM file coordinates (as contig)...
[23:36:32] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[23:38:31] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta
[23:38:31] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.index
[23:38:31] [Teaser      ] remove mapping_comparison_unfixed.sam
[23:38:31] [Teaser      ] Took 476 seconds for generating f2a6f25cabc55338e734f1adbe44516b
[23:38:31] [Main        ] Data set creation completed
[23:38:31] [Main        ] 
[23:38:33] [bowtie2     ] f2a6f25cabc55338e734f1adbe44516b (base: tests_base/base_mapping)
[23:38:33] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[23:38:33] [init        ] Reads: /project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b/reads.fastq
[23:38:33] [init        ] Output:/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b/out_bowtie2.sam
[23:38:33] [map         ] Command(pre): 
[23:38:33] [map         ] Base run time file not existing, performing base run
[23:38:33] [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
[23:39:01] [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
[23:39:01] [map         ]    Mapping 83.00MB to 146.00MB with bowtie2...
[23:39:54] [map         ]    Took 52.726 (wall), 139.156 (CPU) seconds, initialization time: 9.539 (wall), 9.304 (CPU) seconds.
[23:39:54] [map         ] Command(post): 
[23:39:54] [sort_prepare] Sorting...
[23:40:53] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[23:42:01] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
527787,69170,1901,0,0,598858,0,0,0.884129007617,0.996411094833,0.936918017654

[23:42:02] [bwa         ] f2a6f25cabc55338e734f1adbe44516b (base: tests_base/base_mapping)
[23:42:02] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[23:42:02] [init        ] Reads: /project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b/reads.fastq
[23:42:02] [init        ] Output:/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b/out_bwa.sam
[23:42:02] [map         ] Command(pre): 
[23:42:02] [map         ] Base run time file not existing, performing base run
[23:42:02] [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
[23:42:53] [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
[23:42:53] [map         ]    Mapping 83.00MB to 146.00MB with bwa...
[23:44:42] [map         ]    Took 108.689 (wall), 206.048 (CPU) seconds, initialization time: 20.149 (wall), 19.572 (CPU) seconds.
[23:44:42] [map         ] Command(post): 
[23:44:42] [sort_prepare] Sorting...
[23:45:02] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[23:46:08] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
524053,68528,6277,0,0,598858,0,0,0.884356737729,0.988163973375,0.933382966237

[23:46:08] [bwamem      ] f2a6f25cabc55338e734f1adbe44516b (base: tests_base/base_mapping)
[23:46:08] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[23:46:08] [init        ] Reads: /project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b/reads.fastq
[23:46:08] [init        ] Output:/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b/out_bwamem.sam
[23:46:08] [map         ] Command(pre): 
[23:46:09] [map         ] Base run time file not existing, performing base run
[23:46:09] [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
[23:46:32] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwamem.sam
[23:46:32] [map         ]    Mapping 83.00MB to 146.00MB with bwamem...
[23:47:47] [map         ]    Took 74.832 (wall), 180.552 (CPU) seconds, initialization time: 14.391 (wall), 14.016 (CPU) seconds.
[23:47:47] [map         ] Command(post): 
[23:47:47] [sort_prepare] Sorting...
[23:48:07] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[23:49:13] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
529307,69445,106,0,0,598858,0,0,0.884017088878,0.999799778245,0.938350329961

[23:49:13] [bwasw       ] f2a6f25cabc55338e734f1adbe44516b (base: tests_base/base_mapping)
[23:49:13] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[23:49:13] [init        ] Reads: /project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b/reads.fastq
[23:49:13] [init        ] Output:/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b/out_bwasw.sam
[23:49:13] [map         ] Command(pre): 
[23:49:13] [map         ] Base run time file not existing, performing base run
[23:49:13] [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
[23:49:46] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwasw.sam
[23:49:46] [map         ]    Mapping 83.00MB to 146.00MB with bwasw...
[23:51:41] [map         ]    Took 114.517 (wall), 295.204 (CPU) seconds, initialization time: 15.937 (wall), 15.552 (CPU) seconds.
[23:51:41] [map         ] Command(post): 
[23:51:41] [sort_prepare] Sorting...
[23:52:00] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[23:53:05] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
514683,68775,15400,0,24,598858,0,0,0.88212519153,0.970947945888,0.924407812555

[23:53:05] [ngm         ] f2a6f25cabc55338e734f1adbe44516b (base: tests_base/base_mapping)
[23:53:05] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[23:53:05] [init        ] Reads: /project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b/reads.fastq
[23:53:05] [init        ] Output:/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b/out_ngm.sam
[23:53:05] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/D_melanogaster.fasta 
[23:54:16] [map         ] Base run time file not existing, performing base run
[23:54:16] [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
[23:56:35] [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
[23:56:35] [map         ]    Mapping 83.00MB to 146.00MB with ngm...
[23:58:20] [map         ]    Took 104.892 (wall), 195.320 (CPU) seconds, initialization time: 68.526 (wall), 106.016 (CPU) seconds.
[23:58:20] [map         ] Command(post): 
[23:58:21] [sort_prepare] Sorting...
[23:58:47] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[23:59:52] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
529197,68970,691,0,0,598858,0,0,0.884697751631,0.998695950842,0.938246805342