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
D_melanogasterD_melanogaster5500
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 Accessione06f9a576d69697f7ad166f2c53eac4f
Report timestampThu Jul 20 09:07:28 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/e06f9a576d69697f7ad166f2c53eac4f.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 101}
include: [base_teaser.yaml]
meta_timestamp: 1500533332.232679
report: {name: e06f9a576d69697f7ad166f2c53eac4f}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    e06f9a576d69697f7ad166f2c53eac4f: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 101,
      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: 202,
      reference: !!python/unicode 'D_melanogaster.fasta', title: !!python/unicode 'D_melanogaster',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[08:48:54] [Main        ] framework cmd:  ./teaser.py setups_generated/e06f9a576d69697f7ad166f2c53eac4f.yaml -mcpu
[08:48:54] [Main        ] framework hash: vevev
[08:48:54] [Main        ] deployment mode: devel (True)
[08:48:54] [Main        ] Test Runner Setup - ""

[08:48:55] [Main        ] Using Teaser for data set creation
[08:48:55] [Teaser      ] Init. Creating 1 test datasets.
[08:48:55] [Teaser      ] 
[08:48:55] [Teaser      ] Creating test e06f9a576d69697f7ad166f2c53eac4f
[08:48:55] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f
[08:48:55] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f
[08:48:55] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[08:48:55] [Teaser      ] csample /project/teaser/genometeaser/references/D_melanogaster.fasta 1510 0.250000
[08:48:55] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[08:48:55] [Teaser      ] Sampling as contig: 23795 regions of size 1510 (pad 302), totalling 35931498 base pairs
[08:48:55] [Teaser      ] Sampling 23795 regions
[08:49:14] [Teaser      ] 10%
[08:49:19] [Teaser      ] 20%
[08:49:24] [Teaser      ] 30%
[08:49:30] [Teaser      ] 40%
[08:49:35] [Teaser      ] 50%
[08:49:41] [Teaser      ] 60%
[08:49:47] [Teaser      ] 70%
[08:49:53] [Teaser      ] 80%
[08:49:58] [Teaser      ] 90%
[08:50:04] [Teaser      ] 100%
[08:50:06] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f
[08:50:06] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 202 -N 88939 --mp  --ll 101 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1510.302.fasta
[08:50:06] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 202 -N 88939 --mp  --ll 101 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1510.302.fasta
[08:55:30] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1510.302.fasta_1.fastq -> ./reads1.fastq
[08:55:30] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1510.302.fasta_2.fastq -> ./reads2.fastq
[08:55:30] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1510.302.fasta.fastq.sam -> ./mapping_comparison.sam
[08:55:30] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f
[08:55:30] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[08:55:30] [Teaser      ] Translating SAM file coordinates (as contig)...
[08:55:30] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[08:56:06] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1510.302.fasta
[08:56:06] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1510.302.fasta.index
[08:56:06] [Teaser      ] remove mapping_comparison_unfixed.sam
[08:56:06] [Teaser      ] Took 430 seconds for generating e06f9a576d69697f7ad166f2c53eac4f
[08:56:06] [Main        ] Data set creation completed
[08:56:06] [Main        ] 
[08:56:08] [bowtie2     ] e06f9a576d69697f7ad166f2c53eac4f (base: tests_base/base_mapping)
[08:56:08] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[08:56:08] [init        ] Reads: /project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f/reads1.fastq
[08:56:08] [init        ] Output:/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f/out_bowtie2.sam
[08:56:08] [map         ] Command(pre): 
[08:56:08] [map         ] Base run time file not existing, performing base run
[08:56:08] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
[08:56:30] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
[08:56:30] [map         ]    Mapping 75.00MB to 146.00MB with bowtie2...
[08:57:34] [map         ]    Took 63.455 (wall), 224.776 (CPU) seconds, initialization time: 3.428 (wall), 3.328 (CPU) seconds.
[08:57:34] [map         ] Command(post): 
[08:57:34] [sort_prepare] Sorting...
[08:57:56] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 101)... 
[08:58:20] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
163960,13913,5,0,0,177878,0,0,0.921781270907,0.999969505687,0.959284807423

[08:58:20] [bwa         ] e06f9a576d69697f7ad166f2c53eac4f (base: tests_base/base_mapping)
[08:58:20] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[08:58:20] [init        ] Reads: /project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f/reads1.fastq
[08:58:20] [init        ] Output:/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f/out_bwa.sam
[08:58:20] [map         ] Command(pre): 
[08:58:21] [map         ] Base run time file not existing, performing base run
[08:58:21] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[08:58:54] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq  -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads2.fastq  -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
[08:58:54] [map         ]    Mapping 75.00MB to 146.00MB with bwa...
[09:00:16] [map         ]    Took 81.585 (wall), 178.664 (CPU) seconds, initialization time: 6.739 (wall), 6.504 (CPU) seconds.
[09:00:16] [map         ] Command(post): 
[09:00:16] [sort_prepare] Sorting...
[09:00:27] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 101)... 
[09:00:50] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
153739,12650,11489,0,0,177878,0,0,0.923973339584,0.930465780618,0.927208194996

[09:00:50] [bwamem      ] e06f9a576d69697f7ad166f2c53eac4f (base: tests_base/base_mapping)
[09:00:50] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[09:00:50] [init        ] Reads: /project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f/reads1.fastq
[09:00:50] [init        ] Output:/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f/out_bwamem.sam
[09:00:50] [map         ] Command(pre): 
[09:00:50] [map         ] Base run time file not existing, performing base run
[09:00:51] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq  -t 4 > out_bwamem.sam
[09:01:01] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq  -t 4 > out_bwamem.sam
[09:01:01] [map         ]    Mapping 75.00MB to 146.00MB with bwamem...
[09:01:45] [map         ]    Took 43.375 (wall), 134.788 (CPU) seconds, initialization time: 3.688 (wall), 3.576 (CPU) seconds.
[09:01:45] [map         ] Command(post): 
[09:01:45] [sort_prepare] Sorting...
[09:01:55] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 101)... 
[09:02:18] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
166691,11187,0,0,0,177878,0,0,0.937108580038,1.0,0.967533353262

[09:02:18] [bwasw       ] e06f9a576d69697f7ad166f2c53eac4f (base: tests_base/base_mapping)
[09:02:19] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[09:02:19] [init        ] Reads: /project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f/reads1.fastq
[09:02:19] [init        ] Output:/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f/out_bwasw.sam
[09:02:19] [map         ] Command(pre): 
[09:02:19] [map         ] Base run time file not existing, performing base run
[09:02:19] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq  -t 4 > out_bwasw.sam
[09:02:25] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq  -t 4 > out_bwasw.sam
[09:02:25] [map         ]    Mapping 75.00MB to 146.00MB with bwasw...
[09:04:23] [map         ]    Took 118.003 (wall), 370.756 (CPU) seconds, initialization time: 1.994 (wall), 1.872 (CPU) seconds.
[09:04:23] [map         ] Command(post): 
[09:04:23] [sort_prepare] Sorting...
[09:04:34] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 101)... 
[09:04:57] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
164294,13583,0,1,9,177878,0,0,0.923638244405,1.0,0.960303473994

[09:04:57] [ngm         ] e06f9a576d69697f7ad166f2c53eac4f (base: tests_base/base_mapping)
[09:04:57] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[09:04:57] [init        ] Reads: /project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f/reads1.fastq
[09:04:57] [init        ] Output:/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f/out_ngm.sam
[09:04:57] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/D_melanogaster.fasta 
[09:05:52] [map         ] Base run time file not existing, performing base run
[09:05:52] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads_base.fastq  --no-progress
[09:06:20] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4  --no-progress
[09:06:20] [map         ]    Mapping 75.00MB to 146.00MB with ngm...
[09:06:54] [map         ]    Took 33.380 (wall), 77.300 (CPU) seconds, initialization time: 7.643 (wall), 11.756 (CPU) seconds.
[09:06:54] [map         ] Command(post): 
[09:06:54] [sort_prepare] Sorting...
[09:07:05] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 101)... 
[09:07:28] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
165549,12309,20,0,0,177878,0,0,0.930793104612,0.99987920444,0.964100085317