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.

6 tests executed, 0 fail, 0 aborted, 0 errors total.
StateNameReferenceExecutedOKWarningsErrors
H_sapiensH_sapiens6600
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 Accessionab0014cf05e86cd590ae0b3283410abf
Report timestampFri Oct 19 19:46:57 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/ab0014cf05e86cd590ae0b3283410abf.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 18}
include: [base_teaser.yaml]
meta_timestamp: 1539967390.796052
report: {name: ab0014cf05e86cd590ae0b3283410abf}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    ab0014cf05e86cd590ae0b3283410abf: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 200,
      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: 36,
      reference: !!python/unicode 'H_sapiens.fa', title: !!python/unicode 'H_sapiens',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie, bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[18:43:13] [Main        ] framework cmd:  ./teaser.py setups_generated/ab0014cf05e86cd590ae0b3283410abf.yaml -mcpu
[18:43:13] [Main        ] framework hash: vevev
[18:43:13] [Main        ] deployment mode: devel (True)
[18:43:13] [Main        ] Test Runner Setup - ""

[18:43:13] [Main        ] Using Teaser for data set creation
[18:43:13] [Teaser      ] Init. Creating 1 test datasets.
[18:43:13] [Teaser      ] 
[18:43:13] [Teaser      ] Creating test ab0014cf05e86cd590ae0b3283410abf
[18:43:13] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf
[18:43:13] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf
[18:43:13] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[18:43:13] [Teaser      ] csample /project/teaser/genometeaser/references/H_sapiens.fa 2500 0.010000
[18:43:13] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[18:43:13] [Teaser      ] Sampling as contig: 12548 regions of size 2500 (pad 500), totalling 31371612 base pairs
[18:43:13] [Teaser      ] Sampling 12548 regions
[18:45:21] [Teaser      ] 10%
[18:46:47] [Teaser      ] 20%
[18:47:36] [Teaser      ] 30%
[18:48:04] [Teaser      ] 40%
[18:48:21] [Teaser      ] 50%
[18:48:31] [Teaser      ] 60%
[18:48:38] [Teaser      ] 70%
[18:48:43] [Teaser      ] 80%
[18:48:46] [Teaser      ] 90%
[18:48:49] [Teaser      ] 100%
[18:48:51] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf
[18:48:51] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 36 -N 435716 --mp  --ll 200 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.2500.500.fasta
[18:48:51] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 36 -N 435716 --mp  --ll 200 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.2500.500.fasta
[18:51:00] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.2500.500.fasta_1.fastq -> ./reads1.fastq
[18:51:00] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.2500.500.fasta_2.fastq -> ./reads2.fastq
[18:51:00] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.2500.500.fasta.fastq.sam -> ./mapping_comparison.sam
[18:51:00] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf
[18:51:00] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[18:51:00] [Teaser      ] Translating SAM file coordinates (as contig)...
[18:51:00] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[18:52:44] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.2500.500.fasta
[18:52:44] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.2500.500.fasta.index
[18:52:44] [Teaser      ] remove mapping_comparison_unfixed.sam
[18:52:44] [Teaser      ] Took 570 seconds for generating ab0014cf05e86cd590ae0b3283410abf
[18:52:44] [Main        ] Data set creation completed
[18:52:44] [Main        ] 
[18:52:46] [bowtie      ] ab0014cf05e86cd590ae0b3283410abf (base: tests_base/base_mapping)
[18:52:46] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:52:46] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf/reads1.fastq
[18:52:46] [init        ] Output:/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf/out_bowtie.sam
[18:52:46] [map         ] Command(pre): 
[18:52:46] [map         ] Base run time file not existing, performing base run
[18:52:46] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie --threads 4  -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads_base.fastq out_bowtie.sam
[18:56:14] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie --threads 4  -S /project/teaser/genometeaser/references/H_sapiens.fa_bo -1 reads1.fastq -2 reads2.fastq out_bowtie.sam
[18:56:14] [map         ]    Mapping 80.00MB to 3199.00MB with bowtie...
[18:58:12] [map         ]    Took 117.097 (wall), 197.544 (CPU) seconds, initialization time: 2.581 (wall), 2.512 (CPU) seconds.
[18:58:12] [map         ] Command(post): 
[18:58:12] [sort_prepare] Sorting...
[18:59:10] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[19:00:20] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
658035,51681,161716,0,0,871432,0,0,0.927180731448,0.802725461756,0.860476231262

[19:00:20] [bowtie2     ] ab0014cf05e86cd590ae0b3283410abf (base: tests_base/base_mapping)
[19:00:20] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[19:00:20] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf/reads1.fastq
[19:00:20] [init        ] Output:/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf/out_bowtie2.sam
[19:00:21] [map         ] Command(pre): 
[19:00:21] [map         ] Base run time file not existing, performing base run
[19:00:21] [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
[19:05:15] [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
[19:05:15] [map         ]    Mapping 80.00MB to 3199.00MB with bowtie2...
[19:06:37] [map         ]    Took 81.951 (wall), 312.056 (CPU) seconds, initialization time: 3.688 (wall), 3.684 (CPU) seconds.
[19:06:37] [map         ] Command(post): 
[19:06:37] [sort_prepare] Sorting...
[19:07:05] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[19:07:50] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
826770,41166,3496,0,0,871432,0,0,0.952570235593,0.99578930126,0.97370041962

[19:07:50] [bwa         ] ab0014cf05e86cd590ae0b3283410abf (base: tests_base/base_mapping)
[19:07:50] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[19:07:50] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf/reads1.fastq
[19:07:50] [init        ] Output:/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf/out_bwa.sam
[19:07:50] [map         ] Command(pre): 
[19:07:50] [map         ] Base run time file not existing, performing base run
[19:07:50] [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
[19:15:49] [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
[19:15:49] [map         ]    Mapping 80.00MB to 3199.00MB with bwa...
[19:27:02] [map         ]    Took 672.870 (wall), 792.248 (CPU) seconds, initialization time: 7.585 (wall), 7.424 (CPU) seconds.
[19:27:02] [map         ] Command(post): 
[19:27:03] [sort_prepare] Sorting...
[19:27:34] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[19:28:50] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
831497,38798,1137,0,0,871432,1,0,0.955419714005,0.998634454034,0.97654922783

[19:28:50] [bwamem      ] ab0014cf05e86cd590ae0b3283410abf (base: tests_base/base_mapping)
[19:28:50] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[19:28:50] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf/reads1.fastq
[19:28:50] [init        ] Output:/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf/out_bwamem.sam
[19:28:50] [map         ] Command(pre): 
[19:28:50] [map         ] Base run time file not existing, performing base run
[19:28:50] [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
[19:29:00] [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
[19:29:00] [map         ]    Mapping 80.00MB to 3199.00MB with bwamem...
[19:31:12] [map         ]    Took 131.173 (wall), 448.232 (CPU) seconds, initialization time: 4.634 (wall), 4.556 (CPU) seconds.
[19:31:12] [map         ] Command(post): 
[19:31:13] [sort_prepare] Sorting...
[19:31:36] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[19:32:49] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
833135,37715,582,0,0,871432,0,0,0.956691737957,0.999301921395,0.977532710653

[19:32:50] [bwasw       ] ab0014cf05e86cd590ae0b3283410abf (base: tests_base/base_mapping)
[19:32:50] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[19:32:50] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf/reads1.fastq
[19:32:50] [init        ] Output:/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf/out_bwasw.sam
[19:32:50] [map         ] Command(pre): 
[19:32:50] [map         ] Base run time file not existing, performing base run
[19:32:50] [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
[19:33:00] [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
[19:33:00] [map         ]    Mapping 80.00MB to 3199.00MB with bwasw...
[19:34:19] [map         ]    Took 78.566 (wall), 198.968 (CPU) seconds, initialization time: 4.659 (wall), 4.588 (CPU) seconds.
[19:34:19] [map         ] Command(post): 
[19:34:19] [sort_prepare] Sorting...
[19:34:41] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[19:35:52] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
743310,61894,66228,0,0,871432,2,0,0.923132522938,0.918190375251,0.920654816683

[19:35:52] [ngm         ] ab0014cf05e86cd590ae0b3283410abf (base: tests_base/base_mapping)
[19:35:52] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[19:35:52] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf/reads1.fastq
[19:35:52] [init        ] Output:/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf/out_ngm.sam
[19:35:52] [map         ] Command(pre): 
[19:35:52] [map         ] Base run time file not existing, performing base run
[19:35:52] [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
[19:44:19] [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
[19:44:19] [map         ]    Mapping 80.00MB to 3199.00MB with ngm...
[19:45:15] [map         ]    Took 55.733 (wall), 147.676 (CPU) seconds, initialization time: 8.697 (wall), 8.816 (CPU) seconds.
[19:45:15] [map         ] Command(post): 
[19:45:15] [sort_prepare] Sorting...
[19:45:42] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 18)... 
[19:46:56] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
775148,69118,27150,16,0,871432,11,0,0.918132436933,0.966159706244,0.941534006574