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 Accession24d206dec9772782e6efab15944abfc6
Report timestampMon Aug 14 08:41:40 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/24d206dec9772782e6efab15944abfc6.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1502690317.689672
report: {name: 24d206dec9772782e6efab15944abfc6}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    24d206dec9772782e6efab15944abfc6: {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
[07:58:41] [Main        ] framework cmd:  ./teaser.py setups_generated/24d206dec9772782e6efab15944abfc6.yaml -mcpu
[07:58:41] [Main        ] framework hash: vevev
[07:58:41] [Main        ] deployment mode: devel (True)
[07:58:41] [Main        ] Test Runner Setup - ""

[07:58:41] [Main        ] Using Teaser for data set creation
[07:58:41] [Teaser      ] Init. Creating 1 test datasets.
[07:58:41] [Teaser      ] 
[07:58:41] [Teaser      ] Creating test 24d206dec9772782e6efab15944abfc6
[07:58:41] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6
[07:58:41] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6
[07:58:41] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[07:58:41] [Teaser      ] csample /project/teaser/genometeaser/references/H_sapiens.fa 1500 0.010000
[07:58:42] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[07:58:42] [Teaser      ] Sampling as contig: 20914 regions of size 1500 (pad 300), totalling 31371612 base pairs
[07:58:42] [Teaser      ] Sampling 20914 regions
[08:01:43] [Teaser      ] 10%
[08:03:08] [Teaser      ] 20%
[08:03:45] [Teaser      ] 30%
[08:04:00] [Teaser      ] 40%
[08:04:09] [Teaser      ] 50%
[08:04:14] [Teaser      ] 60%
[08:04:18] [Teaser      ] 70%
[08:04:20] [Teaser      ] 80%
[08:04:23] [Teaser      ] 90%
[08:04:26] [Teaser      ] 100%
[08:04:27] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6
[08:04:27] [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
[08:04:27] [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
[08:06:35] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta_1.fastq -> ./reads1.fastq
[08:06:35] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta_2.fastq -> ./reads2.fastq
[08:06:35] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta.fastq.sam -> ./mapping_comparison.sam
[08:06:35] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6
[08:06:35] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[08:06:35] [Teaser      ] Translating SAM file coordinates (as contig)...
[08:06:35] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[08:07:48] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta
[08:07:48] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta.index
[08:07:48] [Teaser      ] remove mapping_comparison_unfixed.sam
[08:07:49] [Teaser      ] Took 547 seconds for generating 24d206dec9772782e6efab15944abfc6
[08:07:49] [Main        ] Data set creation completed
[08:07:49] [Main        ] 
[08:07:50] [bowtie2     ] 24d206dec9772782e6efab15944abfc6 (base: tests_base/base_mapping)
[08:07:51] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[08:07:51] [init        ] Reads: /project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6/reads1.fastq
[08:07:51] [init        ] Output:/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6/out_bowtie2.sam
[08:07:51] [map         ] Command(pre): 
[08:07:51] [map         ] Base run time file not existing, performing base run
[08:07:51] [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
[08:12:46] [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
[08:12:46] [map         ]    Mapping 73.00MB to 3199.00MB with bowtie2...
[08:13:42] [map         ]    Took 55.554 (wall), 196.928 (CPU) seconds, initialization time: 4.619 (wall), 4.696 (CPU) seconds.
[08:13:42] [map         ] Command(post): 
[08:13:42] [sort_prepare] Sorting...
[08:14:20] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[08:15:08] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
501816,20597,447,0,0,522860,0,0,0.960573339484,0.999110028013,0.979462776526

[08:15:08] [bwa         ] 24d206dec9772782e6efab15944abfc6 (base: tests_base/base_mapping)
[08:15:09] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[08:15:09] [init        ] Reads: /project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6/reads1.fastq
[08:15:09] [init        ] Output:/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6/out_bwa.sam
[08:15:09] [map         ] Command(pre): 
[08:15:09] [map         ] Base run time file not existing, performing base run
[08:15:09] [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
[08:23:10] [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
[08:23:10] [map         ]    Mapping 73.00MB to 3199.00MB with bwa...
[08:25:18] [map         ]    Took 127.791 (wall), 260.464 (CPU) seconds, initialization time: 9.826 (wall), 9.632 (CPU) seconds.
[08:25:18] [map         ] Command(post): 
[08:25:18] [sort_prepare] Sorting...
[08:25:37] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[08:26:24] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
500257,20502,2101,0,0,522860,0,0,0.960630541191,0.995817723615,0.977907707525

[08:26:24] [bwamem      ] 24d206dec9772782e6efab15944abfc6 (base: tests_base/base_mapping)
[08:26:24] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[08:26:24] [init        ] Reads: /project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6/reads1.fastq
[08:26:24] [init        ] Output:/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6/out_bwamem.sam
[08:26:24] [map         ] Command(pre): 
[08:26:24] [map         ] Base run time file not existing, performing base run
[08:26:24] [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
[08:26:37] [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
[08:26:37] [map         ]    Mapping 73.00MB to 3199.00MB with bwamem...
[08:27:42] [map         ]    Took 64.984 (wall), 197.396 (CPU) seconds, initialization time: 4.811 (wall), 4.736 (CPU) seconds.
[08:27:42] [map         ] Command(post): 
[08:27:42] [sort_prepare] Sorting...
[08:27:58] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[08:28:44] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
503942,18918,0,0,0,522860,0,0,0.963818230501,1.0,0.981575805267

[08:28:44] [bwasw       ] 24d206dec9772782e6efab15944abfc6 (base: tests_base/base_mapping)
[08:28:44] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[08:28:44] [init        ] Reads: /project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6/reads1.fastq
[08:28:44] [init        ] Output:/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6/out_bwasw.sam
[08:28:44] [map         ] Command(pre): 
[08:28:44] [map         ] Base run time file not existing, performing base run
[08:28:44] [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
[08:28:56] [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
[08:28:56] [map         ]    Mapping 73.00MB to 3199.00MB with bwasw...
[08:30:08] [map         ]    Took 70.143 (wall), 216.672 (CPU) seconds, initialization time: 5.151 (wall), 5.056 (CPU) seconds.
[08:30:08] [map         ] Command(post): 
[08:30:08] [sort_prepare] Sorting...
[08:30:25] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[08:31:11] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
494278,26892,1687,3,49,522860,0,0,0.948400713779,0.996598550301,0.971902451494

[08:31:11] [ngm         ] 24d206dec9772782e6efab15944abfc6 (base: tests_base/base_mapping)
[08:31:11] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[08:31:11] [init        ] Reads: /project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6/reads1.fastq
[08:31:11] [init        ] Output:/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6/out_ngm.sam
[08:31:11] [map         ] Command(pre): 
[08:31:11] [map         ] Base run time file not existing, performing base run
[08:31:11] [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
[08:39:40] [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
[08:39:40] [map         ]    Mapping 73.00MB to 3199.00MB with ngm...
[08:40:37] [map         ]    Took 56.706 (wall), 142.140 (CPU) seconds, initialization time: 10.523 (wall), 10.920 (CPU) seconds.
[08:40:37] [map         ] Command(post): 
[08:40:37] [sort_prepare] Sorting...
[08:40:53] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[08:41:39] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
489414,27141,6303,2,0,522860,0,0,0.947457676336,0.98728508403,0.966961449097