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 Accession0099470d1042c35fd42f63c3beb9132c
Report timestampWed Dec 5 12:46:07 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/0099470d1042c35fd42f63c3beb9132c.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 50}
include: [base_teaser.yaml]
meta_timestamp: 1544009428.43408
report: {name: 0099470d1042c35fd42f63c3beb9132c}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    0099470d1042c35fd42f63c3beb9132c: {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: 100, 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
[12:30:47] [Main        ] framework cmd:  ./teaser.py setups_generated/0099470d1042c35fd42f63c3beb9132c.yaml -mcpu
[12:30:47] [Main        ] framework hash: vevev
[12:30:47] [Main        ] deployment mode: devel (True)
[12:30:47] [Main        ] Test Runner Setup - ""

[12:30:47] [Main        ] Using Teaser for data set creation
[12:30:48] [Teaser      ] Init. Creating 1 test datasets.
[12:30:48] [Teaser      ] 
[12:30:48] [Teaser      ] Creating test 0099470d1042c35fd42f63c3beb9132c
[12:30:48] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c
[12:30:48] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c
[12:30:48] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[12:30:48] [Teaser      ] csample /project/teaser/genometeaser/references/D_melanogaster.fasta 1000 0.250000
[12:30:48] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[12:30:48] [Teaser      ] Sampling as contig: 35931 regions of size 1000 (pad 200), totalling 35931498 base pairs
[12:30:48] [Teaser      ] Sampling 35931 regions
[12:31:09] [Teaser      ] 10%
[12:31:13] [Teaser      ] 20%
[12:31:17] [Teaser      ] 30%
[12:31:21] [Teaser      ] 40%
[12:31:26] [Teaser      ] 50%
[12:31:30] [Teaser      ] 60%
[12:31:34] [Teaser      ] 70%
[12:31:38] [Teaser      ] 80%
[12:31:42] [Teaser      ] 90%
[12:31:47] [Teaser      ] 100%
[12:31:56] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c
[12:31:58] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 100 -N 359314  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1000.200.fasta
[12:31:58] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 100 -N 359314  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1000.200.fasta
[12:35:30] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1000.200.fasta.fastq -> ./reads.fastq
[12:35:32] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1000.200.fasta.fastq.sam -> ./mapping_comparison.sam
[12:35:34] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c
[12:35:34] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[12:35:34] [Teaser      ] Translating SAM file coordinates (as contig)...
[12:35:34] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[12:36:16] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1000.200.fasta
[12:36:16] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.1000.200.fasta.index
[12:36:16] [Teaser      ] remove mapping_comparison_unfixed.sam
[12:36:16] [Teaser      ] Took 328 seconds for generating 0099470d1042c35fd42f63c3beb9132c
[12:36:16] [Main        ] Data set creation completed
[12:36:16] [Main        ] 
[12:36:18] [bowtie2     ] 0099470d1042c35fd42f63c3beb9132c (base: tests_base/base_mapping)
[12:36:19] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[12:36:19] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c/reads.fastq
[12:36:19] [init        ] Output:/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c/out_bowtie2.sam
[12:36:19] [map         ] Command(pre): 
[12:36:19] [map         ] Base run time file not existing, performing base run
[12:36:19] [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
[12:36:38] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads.fastq -S out_bowtie2.sam
[12:36:38] [map         ]    Mapping 79.00MB to 146.00MB with bowtie2...
[12:37:06] [map         ]    Took 27.030 (wall), 60.440 (CPU) seconds, initialization time: 0.579 (wall), 0.612 (CPU) seconds.
[12:37:06] [map         ] Command(post): 
[12:37:07] [sort_prepare] Sorting...
[12:37:42] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[12:37:58] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
323662,35606,46,0,0,359314,0,0,0.900892926729,0.999857896623,0.947799044183

[12:37:58] [bwa         ] 0099470d1042c35fd42f63c3beb9132c (base: tests_base/base_mapping)
[12:37:58] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[12:37:58] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c/reads.fastq
[12:37:58] [init        ] Output:/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c/out_bwa.sam
[12:37:58] [map         ] Command(pre): 
[12:37:58] [map         ] Base run time file not existing, performing base run
[12:37:58] [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
[12:38:21] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads.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.fastq > out_bwa.sam
[12:38:21] [map         ]    Mapping 79.00MB to 146.00MB with bwa...
[12:39:35] [map         ]    Took 73.720 (wall), 118.084 (CPU) seconds, initialization time: 0.519 (wall), 0.428 (CPU) seconds.
[12:39:35] [map         ] Command(post): 
[12:39:36] [sort_prepare] Sorting...
[12:39:48] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[12:40:04] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
317736,34755,6823,0,0,359314,0,0,0.901401737917,0.978977628105,0.93858946902

[12:40:04] [bwamem      ] 0099470d1042c35fd42f63c3beb9132c (base: tests_base/base_mapping)
[12:40:04] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[12:40:04] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c/reads.fastq
[12:40:04] [init        ] Output:/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c/out_bwamem.sam
[12:40:04] [map         ] Command(pre): 
[12:40:04] [map         ] Base run time file not existing, performing base run
[12:40:04] [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
[12:40:06] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwamem.sam
[12:40:06] [map         ]    Mapping 79.00MB to 146.00MB with bwamem...
[12:40:33] [map         ]    Took 26.537 (wall), 67.700 (CPU) seconds, initialization time: 0.326 (wall), 0.276 (CPU) seconds.
[12:40:33] [map         ] Command(post): 
[12:40:33] [sort_prepare] Sorting...
[12:40:50] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[12:41:08] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
324113,35201,0,0,0,359314,0,0,0.902032762431,1.0,0.948493401636

[12:41:08] [bwasw       ] 0099470d1042c35fd42f63c3beb9132c (base: tests_base/base_mapping)
[12:41:08] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[12:41:08] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c/reads.fastq
[12:41:08] [init        ] Output:/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c/out_bwasw.sam
[12:41:08] [map         ] Command(pre): 
[12:41:09] [map         ] Base run time file not existing, performing base run
[12:41:09] [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
[12:41:11] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwasw.sam
[12:41:11] [map         ]    Mapping 79.00MB to 146.00MB with bwasw...
[12:42:35] [map         ]    Took 83.868 (wall), 215.104 (CPU) seconds, initialization time: 0.404 (wall), 0.276 (CPU) seconds.
[12:42:35] [map         ] Command(post): 
[12:42:43] [sort_prepare] Sorting...
[12:43:06] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[12:43:32] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
322893,36212,209,0,41,359314,0,0,0.899160412693,0.999353145446,0.946612978172

[12:43:32] [ngm         ] 0099470d1042c35fd42f63c3beb9132c (base: tests_base/base_mapping)
[12:43:33] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[12:43:33] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c/reads.fastq
[12:43:33] [init        ] Output:/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c/out_ngm.sam
[12:43:33] [map         ] Command(pre): 
[12:43:33] [map         ] Base run time file not existing, performing base run
[12:43:33] [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
[12:44:39] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads.fastq  --no-progress
[12:44:39] [map         ]    Mapping 79.00MB to 146.00MB with ngm...
[12:45:24] [map         ]    Took 44.921 (wall), 68.068 (CPU) seconds, initialization time: 4.634 (wall), 4.828 (CPU) seconds.
[12:45:24] [map         ] Command(post): 
[12:45:28] [sort_prepare] Sorting...
[12:45:42] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[12:46:07] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
323531,35675,108,0,0,359314,0,0,0.900683730227,0.999666294853,0.947597185306