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
H_sapiensH_sapiens5500
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 Accession293e14569a4a233bf507f46e325e460e
Report timestampMon Nov 26 07:48:44 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/293e14569a4a233bf507f46e325e460e.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1543212367.278694
report: {name: 293e14569a4a233bf507f46e325e460e}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    293e14569a4a233bf507f46e325e460e: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 100,
      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 'H_sapiens.fa', title: !!python/unicode 'H_sapiens',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[07:06:09] [Main        ] framework cmd:  ./teaser.py setups_generated/293e14569a4a233bf507f46e325e460e.yaml -mcpu
[07:06:09] [Main        ] framework hash: vevev
[07:06:09] [Main        ] deployment mode: devel (True)
[07:06:09] [Main        ] Test Runner Setup - ""

[07:06:09] [Main        ] Using Teaser for data set creation
[07:06:10] [Teaser      ] Init. Creating 1 test datasets.
[07:06:10] [Teaser      ] 
[07:06:10] [Teaser      ] Creating test 293e14569a4a233bf507f46e325e460e
[07:06:10] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e
[07:06:10] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e
[07:06:10] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[07:06:10] [Teaser      ] csample /project/teaser/genometeaser/references/H_sapiens.fa 1500 0.010000
[07:06:10] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[07:06:10] [Teaser      ] Sampling as contig: 20914 regions of size 1500 (pad 300), totalling 31371612 base pairs
[07:06:10] [Teaser      ] Sampling 20914 regions
[07:09:17] [Teaser      ] 10%
[07:10:42] [Teaser      ] 20%
[07:11:19] [Teaser      ] 30%
[07:11:35] [Teaser      ] 40%
[07:11:43] [Teaser      ] 50%
[07:11:48] [Teaser      ] 60%
[07:11:51] [Teaser      ] 70%
[07:11:54] [Teaser      ] 80%
[07:11:56] [Teaser      ] 90%
[07:11:59] [Teaser      ] 100%
[07:12:00] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e
[07:12:00] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 261430 --mp  --ll 100 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta
[07:12:00] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 261430 --mp  --ll 100 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta
[07:14:15] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta_1.fastq -> ./reads1.fastq
[07:14:15] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta_2.fastq -> ./reads2.fastq
[07:14:15] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta.fastq.sam -> ./mapping_comparison.sam
[07:14:16] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e
[07:14:16] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[07:14:16] [Teaser      ] Translating SAM file coordinates (as contig)...
[07:14:16] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[07:15:28] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta
[07:15:28] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta.index
[07:15:28] [Teaser      ] remove mapping_comparison_unfixed.sam
[07:15:28] [Teaser      ] Took 558 seconds for generating 293e14569a4a233bf507f46e325e460e
[07:15:28] [Main        ] Data set creation completed
[07:15:28] [Main        ] 
[07:15:30] [bowtie2     ] 293e14569a4a233bf507f46e325e460e (base: tests_base/base_mapping)
[07:15:30] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[07:15:30] [init        ] Reads: /project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e/reads1.fastq
[07:15:30] [init        ] Output:/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e/out_bowtie2.sam
[07:15:30] [map         ] Command(pre): 
[07:15:30] [map         ] Base run time file not existing, performing base run
[07:15:30] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
[07:20:25] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
[07:20:25] [map         ]    Mapping 73.00MB to 3199.00MB with bowtie2...
[07:21:12] [map         ]    Took 46.261 (wall), 150.140 (CPU) seconds, initialization time: 3.838 (wall), 3.848 (CPU) seconds.
[07:21:12] [map         ] Command(post): 
[07:21:12] [sort_prepare] Sorting...
[07:21:53] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[07:22:41] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
500909,21515,436,0,0,522860,0,0,0.958816976249,0.999130339387,0.978558639693

[07:22:41] [bwa         ] 293e14569a4a233bf507f46e325e460e (base: tests_base/base_mapping)
[07:22:41] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[07:22:41] [init        ] Reads: /project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e/reads1.fastq
[07:22:41] [init        ] Output:/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e/out_bwa.sam
[07:22:41] [map         ] Command(pre): 
[07:22:41] [map         ] Base run time file not existing, performing base run
[07:22:41] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[07:30:40] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq  -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads2.fastq  -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
[07:30:40] [map         ]    Mapping 73.00MB to 3199.00MB with bwa...
[07:32:22] [map         ]    Took 101.775 (wall), 192.604 (CPU) seconds, initialization time: 7.883 (wall), 7.732 (CPU) seconds.
[07:32:22] [map         ] Command(post): 
[07:32:22] [sort_prepare] Sorting...
[07:32:43] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[07:33:30] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
499426,21332,2102,0,0,522860,0,0,0.959036635059,0.995808808282,0.977076864987

[07:33:31] [bwamem      ] 293e14569a4a233bf507f46e325e460e (base: tests_base/base_mapping)
[07:33:31] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[07:33:31] [init        ] Reads: /project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e/reads1.fastq
[07:33:31] [init        ] Output:/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e/out_bwamem.sam
[07:33:31] [map         ] Command(pre): 
[07:33:31] [map         ] Base run time file not existing, performing base run
[07:33:31] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -t 4 > out_bwamem.sam
[07:33:41] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq  -t 4 > out_bwamem.sam
[07:33:41] [map         ]    Mapping 73.00MB to 3199.00MB with bwamem...
[07:34:41] [map         ]    Took 59.913 (wall), 178.644 (CPU) seconds, initialization time: 4.791 (wall), 4.724 (CPU) seconds.
[07:34:41] [map         ] Command(post): 
[07:34:41] [sort_prepare] Sorting...
[07:34:56] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[07:35:34] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
503147,19713,0,0,0,522860,0,0,0.962297747007,1.0,0.980786680793

[07:35:34] [bwasw       ] 293e14569a4a233bf507f46e325e460e (base: tests_base/base_mapping)
[07:35:34] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[07:35:34] [init        ] Reads: /project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e/reads1.fastq
[07:35:34] [init        ] Output:/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e/out_bwasw.sam
[07:35:34] [map         ] Command(pre): 
[07:35:34] [map         ] Base run time file not existing, performing base run
[07:35:34] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -t 4 > out_bwasw.sam
[07:35:44] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq  -t 4 > out_bwasw.sam
[07:35:44] [map         ]    Mapping 73.00MB to 3199.00MB with bwasw...
[07:37:26] [map         ]    Took 101.159 (wall), 244.700 (CPU) seconds, initialization time: 4.873 (wall), 4.784 (CPU) seconds.
[07:37:26] [map         ] Command(post): 
[07:37:26] [sort_prepare] Sorting...
[07:37:41] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[07:38:27] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
493350,27857,1651,2,42,522860,0,0,0.946552905084,0.996664653203,0.97096263757

[07:38:27] [ngm         ] 293e14569a4a233bf507f46e325e460e (base: tests_base/base_mapping)
[07:38:27] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[07:38:27] [init        ] Reads: /project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e/reads1.fastq
[07:38:27] [init        ] Output:/project/teaser/genometeaser/tests_generated/293e14569a4a233bf507f46e325e460e/out_ngm.sam
[07:38:27] [map         ] Command(pre): 
[07:38:27] [map         ] Base run time file not existing, performing base run
[07:38:27] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq  --no-progress
[07:46:54] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4  --no-progress
[07:46:54] [map         ]    Mapping 73.00MB to 3199.00MB with ngm...
[07:47:42] [map         ]    Took 47.247 (wall), 126.596 (CPU) seconds, initialization time: 8.893 (wall), 8.992 (CPU) seconds.
[07:47:42] [map         ] Command(post): 
[07:47:42] [sort_prepare] Sorting...
[07:47:58] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[07:48:44] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
486608,30259,5993,0,0,522860,0,0,0.941456893166,0.987833967044,0.964088014677