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
M_musculus_cutfM_musculus_cutf5500
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 Accession9616eba5217c671aa1e17d118aefe3c9
Report timestampWed Sep 13 11:01:21 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/9616eba5217c671aa1e17d118aefe3c9.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 38}
include: [base_teaser.yaml]
meta_timestamp: 1505289969.750937
report: {name: 9616eba5217c671aa1e17d118aefe3c9}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    9616eba5217c671aa1e17d118aefe3c9: {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: 76, reference: !!python/unicode 'M_musculus_cutf.fasta', title: !!python/unicode 'M_musculus_cutf',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[10:06:14] [Main        ] framework cmd:  ./teaser.py setups_generated/9616eba5217c671aa1e17d118aefe3c9.yaml -mcpu
[10:06:14] [Main        ] framework hash: vevev
[10:06:14] [Main        ] deployment mode: devel (True)
[10:06:14] [Main        ] Test Runner Setup - ""

[10:06:15] [Main        ] Using Teaser for data set creation
[10:06:15] [Teaser      ] Init. Creating 1 test datasets.
[10:06:15] [Teaser      ] 
[10:06:15] [Teaser      ] Creating test 9616eba5217c671aa1e17d118aefe3c9
[10:06:15] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9
[10:06:15] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9
[10:06:15] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus_cutf.fasta.teaser.findex
[10:06:15] [Teaser      ] csample /project/teaser/genometeaser/references/M_musculus_cutf.fasta 760 0.010000
[10:06:15] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus_cutf.fasta.teaser.findex
[10:06:15] [Teaser      ] Sampling as contig: 35862 regions of size 760 (pad 152), totalling 27255376 base pairs
[10:06:15] [Teaser      ] Sampling 35862 regions
[10:10:04] [Teaser      ] 10%
[10:10:48] [Teaser      ] 20%
[10:10:59] [Teaser      ] 30%
[10:11:04] [Teaser      ] 40%
[10:11:09] [Teaser      ] 50%
[10:11:13] [Teaser      ] 60%
[10:11:17] [Teaser      ] 70%
[10:11:21] [Teaser      ] 80%
[10:11:24] [Teaser      ] 90%
[10:11:29] [Teaser      ] 100%
[10:11:31] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9
[10:11:31] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 76 -N 358623  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/M_musculus_cutf.fasta.sampled.100.760.152.fasta
[10:11:31] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 76 -N 358623  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/M_musculus_cutf.fasta.sampled.100.760.152.fasta
[10:13:14] [Teaser      ] move /project/teaser/genometeaser/references/M_musculus_cutf.fasta.sampled.100.760.152.fasta.fastq -> ./reads.fastq
[10:13:14] [Teaser      ] move /project/teaser/genometeaser/references/M_musculus_cutf.fasta.sampled.100.760.152.fasta.fastq.sam -> ./mapping_comparison.sam
[10:13:14] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9
[10:13:14] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[10:13:14] [Teaser      ] Translating SAM file coordinates (as contig)...
[10:13:14] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus_cutf.fasta.teaser.findex
[10:13:54] [Teaser      ] remove /project/teaser/genometeaser/references/M_musculus_cutf.fasta.sampled.100.760.152.fasta
[10:13:54] [Teaser      ] remove /project/teaser/genometeaser/references/M_musculus_cutf.fasta.sampled.100.760.152.fasta.index
[10:13:54] [Teaser      ] remove mapping_comparison_unfixed.sam
[10:13:54] [Teaser      ] Took 458 seconds for generating 9616eba5217c671aa1e17d118aefe3c9
[10:13:54] [Main        ] Data set creation completed
[10:13:54] [Main        ] 
[10:13:56] [bowtie2     ] 9616eba5217c671aa1e17d118aefe3c9 (base: tests_base/base_mapping)
[10:13:56] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[10:13:56] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9/reads.fastq
[10:13:56] [init        ] Output:/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9/out_bowtie2.sam
[10:13:56] [map         ] Command(pre): 
[10:13:56] [map         ] Base run time file not existing, performing base run
[10:13:56] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
[10:18:59] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads.fastq -S out_bowtie2.sam
[10:18:59] [map         ]    Mapping 61.00MB to 2770.00MB with bowtie2...
[10:20:41] [map         ]    Took 101.975 (wall), 278.952 (CPU) seconds, initialization time: 36.643 (wall), 36.080 (CPU) seconds.
[10:20:41] [map         ] Command(post): 
[10:20:41] [sort_prepare] Sorting...
[10:21:11] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 38)... 
[10:21:45] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
324263,33818,542,0,0,358623,0,0,0.905557681083,0.998331306476,0.949684134687

[10:21:45] [bwa         ] 9616eba5217c671aa1e17d118aefe3c9 (base: tests_base/base_mapping)
[10:21:45] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[10:21:45] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9/reads.fastq
[10:21:45] [init        ] Output:/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9/out_bwa.sam
[10:21:45] [map         ] Command(pre): 
[10:21:45] [map         ] Base run time file not existing, performing base run
[10:21:45] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[10:31:23] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
[10:31:23] [map         ]    Mapping 61.00MB to 2770.00MB with bwa...
[10:35:27] [map         ]    Took 243.631 (wall), 395.448 (CPU) seconds, initialization time: 116.338 (wall), 114.832 (CPU) seconds.
[10:35:27] [map         ] Command(post): 
[10:35:27] [sort_prepare] Sorting...
[10:35:38] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 38)... 
[10:36:10] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
321236,33123,4264,0,0,358623,0,0,0.906526996633,0.98690015361,0.945007714835

[10:36:11] [bwamem      ] 9616eba5217c671aa1e17d118aefe3c9 (base: tests_base/base_mapping)
[10:36:11] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[10:36:11] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9/reads.fastq
[10:36:11] [init        ] Output:/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9/out_bwamem.sam
[10:36:11] [map         ] Command(pre): 
[10:36:11] [map         ] Base run time file not existing, performing base run
[10:36:11] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq  -t 4 > out_bwamem.sam
[10:38:36] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq  -t 4 > out_bwamem.sam
[10:38:36] [map         ]    Mapping 61.00MB to 2770.00MB with bwamem...
[10:41:17] [map         ]    Took 160.218 (wall), 290.056 (CPU) seconds, initialization time: 89.092 (wall), 88.292 (CPU) seconds.
[10:41:17] [map         ] Command(post): 
[10:41:17] [sort_prepare] Sorting...
[10:41:31] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 38)... 
[10:42:02] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
325450,33168,5,0,0,358623,0,2,0.907511614029,0.999984636893,0.95150663745

[10:42:02] [bwasw       ] 9616eba5217c671aa1e17d118aefe3c9 (base: tests_base/base_mapping)
[10:42:02] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[10:42:02] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9/reads.fastq
[10:42:02] [init        ] Output:/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9/out_bwasw.sam
[10:42:02] [map         ] Command(pre): 
[10:42:02] [map         ] Base run time file not existing, performing base run
[10:42:02] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq  -t 4 > out_bwasw.sam
[10:43:53] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq  -t 4 > out_bwasw.sam
[10:43:53] [map         ]    Mapping 61.00MB to 2770.00MB with bwasw...
[10:47:04] [map         ]    Took 190.430 (wall), 425.120 (CPU) seconds, initialization time: 53.883 (wall), 53.024 (CPU) seconds.
[10:47:04] [map         ] Command(post): 
[10:47:04] [sort_prepare] Sorting...
[10:47:14] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 38)... 
[10:47:46] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
321276,33995,3352,0,30,358623,0,0,0.904312482584,0.989674334931,0.945069782424

[10:47:46] [ngm         ] 9616eba5217c671aa1e17d118aefe3c9 (base: tests_base/base_mapping)
[10:47:46] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[10:47:46] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9/reads.fastq
[10:47:46] [init        ] Output:/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9/out_ngm.sam
[10:47:46] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/M_musculus_cutf.fasta 
[10:55:25] [map         ] Base run time file not existing, performing base run
[10:55:25] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/M_musculus_cutf.fasta -t 4 --qry reads_base.fastq  --no-progress
[10:57:52] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/M_musculus_cutf.fasta -t 4 --qry reads.fastq  --no-progress
[10:57:52] [map         ]    Mapping 61.00MB to 2770.00MB with ngm...
[11:00:35] [map         ]    Took 162.293 (wall), 285.252 (CPU) seconds, initialization time: 70.132 (wall), 82.996 (CPU) seconds.
[11:00:35] [map         ] Command(post): 
[11:00:35] [sort_prepare] Sorting...
[11:00:46] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 38)... 
[11:01:20] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
323225,30684,4714,0,0,358623,0,0,0.913299746545,0.985625375451,0.94808520374