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 Accession550e44394139b4f9ff4d8f5d1ede8a8f
Report timestampTue Nov 13 09:43:36 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/550e44394139b4f9ff4d8f5d1ede8a8f.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 20}
include: [base_teaser.yaml]
meta_timestamp: 1542097463.664695
report: {name: 550e44394139b4f9ff4d8f5d1ede8a8f}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    550e44394139b4f9ff4d8f5d1ede8a8f: {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: 40, 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
[09:24:25] [Main        ] framework cmd:  ./teaser.py setups_generated/550e44394139b4f9ff4d8f5d1ede8a8f.yaml -mcpu
[09:24:25] [Main        ] framework hash: vevev
[09:24:25] [Main        ] deployment mode: devel (True)
[09:24:25] [Main        ] Test Runner Setup - ""

[09:24:25] [Main        ] Using Teaser for data set creation
[09:24:25] [Teaser      ] Init. Creating 1 test datasets.
[09:24:25] [Teaser      ] 
[09:24:25] [Teaser      ] Creating test 550e44394139b4f9ff4d8f5d1ede8a8f
[09:24:25] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f
[09:24:25] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f
[09:24:25] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[09:24:25] [Teaser      ] csample /project/teaser/genometeaser/references/H_sapiens.fa 400 0.010000
[09:24:25] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[09:24:25] [Teaser      ] Sampling as contig: 78429 regions of size 400 (pad 80), totalling 31371612 base pairs
[09:24:25] [Teaser      ] Sampling 78429 regions
[09:24:33] [Teaser      ] 10%
[09:24:39] [Teaser      ] 20%
[09:24:45] [Teaser      ] 30%
[09:24:52] [Teaser      ] 40%
[09:24:58] [Teaser      ] 50%
[09:25:04] [Teaser      ] 60%
[09:25:11] [Teaser      ] 70%
[09:25:17] [Teaser      ] 80%
[09:25:24] [Teaser      ] 90%
[09:25:32] [Teaser      ] 100%
[09:25:36] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f
[09:25:36] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 40 -N 784290  --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.100.400.80.fasta
[09:25:36] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 40 -N 784290  --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.100.400.80.fasta
[09:26:43] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.400.80.fasta.fastq -> ./reads.fastq
[09:26:43] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.400.80.fasta.fastq.sam -> ./mapping_comparison.sam
[09:26:43] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f
[09:26:43] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[09:26:43] [Teaser      ] Translating SAM file coordinates (as contig)...
[09:26:43] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[09:27:59] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.400.80.fasta
[09:28:01] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.400.80.fasta.index
[09:28:02] [Teaser      ] remove mapping_comparison_unfixed.sam
[09:28:03] [Teaser      ] Took 218 seconds for generating 550e44394139b4f9ff4d8f5d1ede8a8f
[09:28:09] [Main        ] Data set creation completed
[09:28:09] [Main        ] 
[09:28:10] [bowtie      ] 550e44394139b4f9ff4d8f5d1ede8a8f (base: tests_base/base_mapping)
[09:28:10] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[09:28:10] [init        ] Reads: /project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f/reads.fastq
[09:28:10] [init        ] Output:/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f/out_bowtie.sam
[09:28:10] [map         ] Command(pre): 
[09:28:10] [map         ] Base run time file not existing, performing base run
[09:28:10] [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
[09:28:15] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie --threads 4  -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads.fastq out_bowtie.sam
[09:28:15] [map         ]    Mapping 78.00MB to 3199.00MB with bowtie...
[09:28:39] [map         ]    Took 23.674 (wall), 46.596 (CPU) seconds, initialization time: 1.579 (wall), 1.512 (CPU) seconds.
[09:28:39] [map         ] Command(post): 
[09:28:40] [sort_prepare] Sorting...
[09:29:27] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[09:30:19] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
648669,82810,52811,0,0,784290,4,0,0.886791008354,0.924714888521,0.905355980178

[09:30:19] [bowtie2     ] 550e44394139b4f9ff4d8f5d1ede8a8f (base: tests_base/base_mapping)
[09:30:19] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[09:30:19] [init        ] Reads: /project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f/reads.fastq
[09:30:19] [init        ] Output:/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f/out_bowtie2.sam
[09:30:19] [map         ] Command(pre): 
[09:30:19] [map         ] Base run time file not existing, performing base run
[09:30:19] [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
[09:30:27] [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
[09:30:27] [map         ]    Mapping 78.00MB to 3199.00MB with bowtie2...
[09:31:08] [map         ]    Took 39.666 (wall), 97.412 (CPU) seconds, initialization time: 3.635 (wall), 3.632 (CPU) seconds.
[09:31:08] [map         ] Command(post): 
[09:31:08] [sort_prepare] Sorting...
[09:31:33] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[09:32:20] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
686063,82401,15826,0,0,784290,3,0,0.892771814945,0.977452275217,0.933194953865

[09:32:20] [bwa         ] 550e44394139b4f9ff4d8f5d1ede8a8f (base: tests_base/base_mapping)
[09:32:20] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[09:32:20] [init        ] Reads: /project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f/reads.fastq
[09:32:20] [init        ] Output:/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f/out_bwa.sam
[09:32:20] [map         ] Command(pre): 
[09:32:21] [map         ] Base run time file not existing, performing base run
[09:32:21] [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
[09:32:35] [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
[09:32:35] [map         ]    Mapping 78.00MB to 3199.00MB with bwa...
[09:34:23] [map         ]    Took 107.147 (wall), 217.440 (CPU) seconds, initialization time: 6.136 (wall), 5.996 (CPU) seconds.
[09:34:23] [map         ] Command(post): 
[09:34:28] [sort_prepare] Sorting...
[09:35:02] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[09:35:59] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
696470,83552,4268,0,0,784290,2,0,0.892885072472,0.993909278504,0.940692617305

[09:35:59] [bwamem      ] 550e44394139b4f9ff4d8f5d1ede8a8f (base: tests_base/base_mapping)
[09:35:59] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[09:35:59] [init        ] Reads: /project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f/reads.fastq
[09:35:59] [init        ] Output:/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f/out_bwamem.sam
[09:35:59] [map         ] Command(pre): 
[09:35:59] [map         ] Base run time file not existing, performing base run
[09:35:59] [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
[09:36:11] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq  -t 4 > out_bwamem.sam
[09:36:11] [map         ]    Mapping 78.00MB to 3199.00MB with bwamem...
[09:37:19] [map         ]    Took 67.912 (wall), 210.180 (CPU) seconds, initialization time: 4.878 (wall), 4.812 (CPU) seconds.
[09:37:19] [map         ] Command(post): 
[09:37:19] [sort_prepare] Sorting...
[09:37:38] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[09:38:24] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
692097,82815,9378,0,0,784290,3,0,0.893129800545,0.986631027478,0.937554990663

[09:38:24] [bwasw       ] 550e44394139b4f9ff4d8f5d1ede8a8f (base: tests_base/base_mapping)
[09:38:24] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[09:38:24] [init        ] Reads: /project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f/reads.fastq
[09:38:24] [init        ] Output:/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f/out_bwasw.sam
[09:38:24] [map         ] Command(pre): 
[09:38:24] [map         ] Base run time file not existing, performing base run
[09:38:25] [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
[09:38:36] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq  -t 4 > out_bwasw.sam
[09:38:36] [map         ]    Mapping 78.00MB to 3199.00MB with bwasw...
[09:39:39] [map         ]    Took 62.049 (wall), 163.888 (CPU) seconds, initialization time: 4.890 (wall), 4.792 (CPU) seconds.
[09:39:39] [map         ] Command(post): 
[09:39:39] [sort_prepare] Sorting...
[09:39:58] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[09:40:49] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
586076,76050,122164,0,1,784290,2,0,0.885142706977,0.827510448436,0.855356890057

[09:40:49] [ngm         ] 550e44394139b4f9ff4d8f5d1ede8a8f (base: tests_base/base_mapping)
[09:40:49] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[09:40:49] [init        ] Reads: /project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f/reads.fastq
[09:40:49] [init        ] Output:/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f/out_ngm.sam
[09:40:49] [map         ] Command(pre): 
[09:40:49] [map         ] Base run time file not existing, performing base run
[09:40:49] [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
[09:41:07] [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
[09:41:07] [map         ]    Mapping 78.00MB to 3199.00MB with ngm...
[09:42:07] [map         ]    Took 59.590 (wall), 141.640 (CPU) seconds, initialization time: 8.044 (wall), 8.160 (CPU) seconds.
[09:42:07] [map         ] Command(post): 
[09:42:08] [sort_prepare] Sorting...
[09:42:31] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[09:43:36] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
689681,73534,21075,0,0,784290,1,0,0.903652312913,0.970348474019,0.93581352686