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
Arabidopsis_thalianaArabidopsis_thaliana5500
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 Accession337f8b971fac4ff7ee4490260598b300
Report timestampMon Nov 5 11:35:02 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/337f8b971fac4ff7ee4490260598b300.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 50}
include: [base_teaser.yaml]
meta_timestamp: 1541413411.752613
report: {name: 337f8b971fac4ff7ee4490260598b300}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    337f8b971fac4ff7ee4490260598b300: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 400,
      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: 100,
      reference: !!python/unicode 'Arabidopsis_thaliana.fas', title: !!python/unicode 'Arabidopsis_thaliana',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[11:23:34] [Main        ] framework cmd:  ./teaser.py setups_generated/337f8b971fac4ff7ee4490260598b300.yaml -mcpu
[11:23:34] [Main        ] framework hash: vevev
[11:23:34] [Main        ] deployment mode: devel (True)
[11:23:34] [Main        ] Test Runner Setup - ""

[11:23:34] [Main        ] Using Teaser for data set creation
[11:23:34] [Teaser      ] Init. Creating 1 test datasets.
[11:23:34] [Teaser      ] 
[11:23:34] [Teaser      ] Creating test 337f8b971fac4ff7ee4490260598b300
[11:23:34] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300
[11:23:34] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300
[11:23:35] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.teaser.findex
[11:23:35] [Teaser      ] csample /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 4500 0.250000
[11:23:35] [Teaser      ] Sampled file exists, skip sampling
[11:23:35] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300
[11:23:35] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 100 -N 149584 --mp  --ll 400 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4500.900.fasta
[11:23:35] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 100 -N 149584 --mp  --ll 400 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4500.900.fasta
[11:26:15] [Teaser      ] move /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4500.900.fasta_1.fastq -> ./reads1.fastq
[11:26:15] [Teaser      ] move /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4500.900.fasta_2.fastq -> ./reads2.fastq
[11:26:15] [Teaser      ] move /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4500.900.fasta.fastq.sam -> ./mapping_comparison.sam
[11:26:15] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300
[11:26:15] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[11:26:15] [Teaser      ] Translating SAM file coordinates (as contig)...
[11:26:15] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.teaser.findex
[11:26:59] [Teaser      ] remove /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4500.900.fasta
[11:26:59] [Teaser      ] remove /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.sampled.4.4500.900.fasta.index
[11:26:59] [Teaser      ] remove mapping_comparison_unfixed.sam
[11:26:59] [Teaser      ] Took 204 seconds for generating 337f8b971fac4ff7ee4490260598b300
[11:26:59] [Main        ] Data set creation completed
[11:26:59] [Main        ] 
[11:27:02] [bowtie2     ] 337f8b971fac4ff7ee4490260598b300 (base: tests_base/base_mapping)
[11:27:02] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[11:27:02] [init        ] Reads: /project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300/reads1.fastq
[11:27:02] [init        ] Output:/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300/out_bowtie2.sam
[11:27:02] [map         ] Command(pre): 
[11:27:02] [map         ] Base run time file not existing, performing base run
[11:27:02] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam
[11:27:17] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
[11:27:17] [map         ]    Mapping 65.00MB to 121.00MB with bowtie2...
[11:27:43] [map         ]    Took 25.946 (wall), 89.652 (CPU) seconds, initialization time: 0.490 (wall), 0.536 (CPU) seconds.
[11:27:43] [map         ] Command(post): 
[11:27:43] [sort_prepare] Sorting...
[11:28:11] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[11:28:41] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
295268,3882,18,0,0,299168,0,0,0.987023232492,0.999939042149,0.993439159136

[11:28:41] [bwa         ] 337f8b971fac4ff7ee4490260598b300 (base: tests_base/base_mapping)
[11:28:41] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[11:28:41] [init        ] Reads: /project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300/reads1.fastq
[11:28:41] [init        ] Output:/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300/out_bwa.sam
[11:28:41] [map         ] Command(pre): 
[11:28:41] [map         ] Base run time file not existing, performing base run
[11:28:41] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[11:29:02] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq  -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads2.fastq  -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
[11:29:02] [map         ]    Mapping 65.00MB to 121.00MB with bwa...
[11:29:46] [map         ]    Took 43.940 (wall), 78.400 (CPU) seconds, initialization time: 0.400 (wall), 0.304 (CPU) seconds.
[11:29:46] [map         ] Command(post): 
[11:29:46] [sort_prepare] Sorting...
[11:29:57] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[11:30:26] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
294931,3924,313,0,0,299168,0,0,0.986869886734,0.998939859912,0.992868192002

[11:30:27] [bwamem      ] 337f8b971fac4ff7ee4490260598b300 (base: tests_base/base_mapping)
[11:30:27] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[11:30:27] [init        ] Reads: /project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300/reads1.fastq
[11:30:27] [init        ] Output:/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300/out_bwamem.sam
[11:30:27] [map         ] Command(pre): 
[11:30:27] [map         ] Base run time file not existing, performing base run
[11:30:27] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq  -t 4 > out_bwamem.sam
[11:30:29] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq  -t 4 > out_bwamem.sam
[11:30:29] [map         ]    Mapping 65.00MB to 121.00MB with bwamem...
[11:30:49] [map         ]    Took 19.695 (wall), 44.588 (CPU) seconds, initialization time: 0.251 (wall), 0.200 (CPU) seconds.
[11:30:49] [map         ] Command(post): 
[11:30:49] [sort_prepare] Sorting...
[11:31:00] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[11:31:28] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
295230,3938,0,0,0,299168,0,0,0.986836827468,1.0,0.993374809471

[11:31:29] [bwasw       ] 337f8b971fac4ff7ee4490260598b300 (base: tests_base/base_mapping)
[11:31:29] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[11:31:29] [init        ] Reads: /project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300/reads1.fastq
[11:31:29] [init        ] Output:/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300/out_bwasw.sam
[11:31:29] [map         ] Command(pre): 
[11:31:29] [map         ] Base run time file not existing, performing base run
[11:31:29] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq  -t 4 > out_bwasw.sam
[11:31:31] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq  -t 4 > out_bwasw.sam
[11:31:31] [map         ]    Mapping 65.00MB to 121.00MB with bwasw...
[11:32:19] [map         ]    Took 47.638 (wall), 152.528 (CPU) seconds, initialization time: 0.259 (wall), 0.204 (CPU) seconds.
[11:32:19] [map         ] Command(post): 
[11:32:19] [sort_prepare] Sorting...
[11:32:30] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[11:32:58] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
293215,5951,2,0,2,299168,0,0,0.980108033667,0.999993179113,0.989950758209

[11:32:58] [ngm         ] 337f8b971fac4ff7ee4490260598b300 (base: tests_base/base_mapping)
[11:32:58] [init        ] Ref:   /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas
[11:32:58] [init        ] Reads: /project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300/reads1.fastq
[11:32:58] [init        ] Output:/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300/out_ngm.sam
[11:32:58] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 
[11:33:47] [map         ] Base run time file not existing, performing base run
[11:33:47] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas -t 4 --qry reads_base.fastq  --no-progress
[11:33:58] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas -t 4  --no-progress
[11:33:58] [map         ]    Mapping 65.00MB to 121.00MB with ngm...
[11:34:19] [map         ]    Took 20.444 (wall), 36.072 (CPU) seconds, initialization time: 3.147 (wall), 3.292 (CPU) seconds.
[11:34:19] [map         ] Command(post): 
[11:34:19] [sort_prepare] Sorting...
[11:34:33] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[11:35:02] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
294585,4576,7,0,0,299168,0,0,0.984703888542,0.999976238323,0.992281302158