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 Accession0ae17b2547a4a7bf1a0dbd8dcfe180bb
Report timestampMon Oct 8 14:20:34 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 25}
include: [base_teaser.yaml]
meta_timestamp: 1539000107.374149
report: {name: 0ae17b2547a4a7bf1a0dbd8dcfe180bb}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    0ae17b2547a4a7bf1a0dbd8dcfe180bb: {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: 50, 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
[14:01:48] [Main        ] framework cmd:  ./teaser.py setups_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb.yaml -mcpu
[14:01:48] [Main        ] framework hash: vevev
[14:01:48] [Main        ] deployment mode: devel (True)
[14:01:48] [Main        ] Test Runner Setup - ""

[14:01:49] [Main        ] Using Teaser for data set creation
[14:01:49] [Teaser      ] Init. Creating 1 test datasets.
[14:01:49] [Teaser      ] 
[14:01:49] [Teaser      ] Creating test 0ae17b2547a4a7bf1a0dbd8dcfe180bb
[14:01:49] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb
[14:01:49] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb
[14:01:49] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[14:01:49] [Teaser      ] csample /project/teaser/genometeaser/references/H_sapiens.fa 500 0.010000
[14:01:49] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[14:01:49] [Teaser      ] Sampling as contig: 62743 regions of size 500 (pad 100), totalling 31371612 base pairs
[14:01:49] [Teaser      ] Sampling 62743 regions
[14:01:55] [Teaser      ] 10%
[14:02:02] [Teaser      ] 20%
[14:02:09] [Teaser      ] 30%
[14:02:16] [Teaser      ] 40%
[14:02:23] [Teaser      ] 50%
[14:02:31] [Teaser      ] 60%
[14:02:38] [Teaser      ] 70%
[14:02:45] [Teaser      ] 80%
[14:02:52] [Teaser      ] 90%
[14:03:00] [Teaser      ] 100%
[14:03:02] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb
[14:03:02] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 50 -N 627432  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.500.100.fasta
[14:03:02] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 50 -N 627432  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.500.100.fasta
[14:05:10] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.500.100.fasta.fastq -> ./reads.fastq
[14:05:10] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.500.100.fasta.fastq.sam -> ./mapping_comparison.sam
[14:05:10] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb
[14:05:10] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[14:05:10] [Teaser      ] Translating SAM file coordinates (as contig)...
[14:05:10] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[14:06:48] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.500.100.fasta
[14:06:48] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.500.100.fasta.index
[14:06:48] [Teaser      ] remove mapping_comparison_unfixed.sam
[14:06:48] [Teaser      ] Took 298 seconds for generating 0ae17b2547a4a7bf1a0dbd8dcfe180bb
[14:06:48] [Main        ] Data set creation completed
[14:06:48] [Main        ] 
[14:06:48] [bowtie2     ] 0ae17b2547a4a7bf1a0dbd8dcfe180bb (base: tests_base/base_mapping)
[14:06:48] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[14:06:48] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb/reads.fastq
[14:06:48] [init        ] Output:/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb/out_bowtie2.sam
[14:06:48] [map         ] Command(pre): 
[14:06:48] [map         ] Base run time file not existing, performing base run
[14:06:48] [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
[14:06:57] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads.fastq -S out_bowtie2.sam
[14:06:57] [map         ]    Mapping 75.00MB to 3199.00MB with bowtie2...
[14:07:42] [map         ]    Took 44.042 (wall), 120.892 (CPU) seconds, initialization time: 3.360 (wall), 3.408 (CPU) seconds.
[14:07:42] [map         ] Command(post): 
[14:07:42] [sort_prepare] Sorting...
[14:08:30] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:09:24] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
573186,49255,4991,0,0,627432,1,0,0.920868001947,0.99136769536,0.954818268592

[14:09:24] [bwa         ] 0ae17b2547a4a7bf1a0dbd8dcfe180bb (base: tests_base/base_mapping)
[14:09:24] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[14:09:24] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb/reads.fastq
[14:09:24] [init        ] Output:/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb/out_bwa.sam
[14:09:24] [map         ] Command(pre): 
[14:09:24] [map         ] Base run time file not existing, performing base run
[14:09:24] [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
[14:09:40] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads.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.fastq > out_bwa.sam
[14:09:40] [map         ]    Mapping 75.00MB to 3199.00MB with bwa...
[14:11:27] [map         ]    Took 106.983 (wall), 235.044 (CPU) seconds, initialization time: 7.072 (wall), 6.960 (CPU) seconds.
[14:11:27] [map         ] Command(post): 
[14:11:27] [sort_prepare] Sorting...
[14:11:44] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:12:37] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
574153,48521,4758,0,0,627432,0,0,0.922076399528,0.991781120069,0.955659399876

[14:12:37] [bwamem      ] 0ae17b2547a4a7bf1a0dbd8dcfe180bb (base: tests_base/base_mapping)
[14:12:37] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[14:12:37] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb/reads.fastq
[14:12:37] [init        ] Output:/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb/out_bwamem.sam
[14:12:38] [map         ] Command(pre): 
[14:12:38] [map         ] Base run time file not existing, performing base run
[14:12:38] [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
[14:12:48] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq  -t 4 > out_bwamem.sam
[14:12:48] [map         ]    Mapping 75.00MB to 3199.00MB with bwamem...
[14:13:49] [map         ]    Took 60.756 (wall), 184.988 (CPU) seconds, initialization time: 4.587 (wall), 4.524 (CPU) seconds.
[14:13:49] [map         ] Command(post): 
[14:13:49] [sort_prepare] Sorting...
[14:14:05] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:14:56] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
577832,48831,769,0,0,627432,1,1,0.922077735561,0.998670932128,0.958847190325

[14:14:57] [bwasw       ] 0ae17b2547a4a7bf1a0dbd8dcfe180bb (base: tests_base/base_mapping)
[14:14:57] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[14:14:57] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb/reads.fastq
[14:14:57] [init        ] Output:/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb/out_bwasw.sam
[14:14:57] [map         ] Command(pre): 
[14:14:57] [map         ] Base run time file not existing, performing base run
[14:14:57] [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
[14:15:07] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq  -t 4 > out_bwasw.sam
[14:15:07] [map         ]    Mapping 75.00MB to 3199.00MB with bwasw...
[14:17:00] [map         ]    Took 113.065 (wall), 242.160 (CPU) seconds, initialization time: 4.728 (wall), 4.540 (CPU) seconds.
[14:17:00] [map         ] Command(post): 
[14:17:00] [sort_prepare] Sorting...
[14:17:16] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:18:06] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
528469,47953,51010,0,14,627432,0,0,0.916809212695,0.911972651295,0.914384536392

[14:18:06] [ngm         ] 0ae17b2547a4a7bf1a0dbd8dcfe180bb (base: tests_base/base_mapping)
[14:18:06] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[14:18:06] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb/reads.fastq
[14:18:06] [init        ] Output:/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb/out_ngm.sam
[14:18:06] [map         ] Command(pre): 
[14:18:06] [map         ] Base run time file not existing, performing base run
[14:18:06] [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
[14:18:23] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads.fastq  --no-progress
[14:18:23] [map         ]    Mapping 75.00MB to 3199.00MB with ngm...
[14:19:21] [map         ]    Took 57.439 (wall), 147.052 (CPU) seconds, initialization time: 7.800 (wall), 8.024 (CPU) seconds.
[14:19:21] [map         ] Command(post): 
[14:19:21] [sort_prepare] Sorting...
[14:19:39] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:20:33] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
570096,46093,11243,0,0,627432,0,0,0.925196652326,0.980660165583,0.952121370022