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
D_melanogasterD_melanogaster6600
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 Accessionbe9adfa40f58b4dfd03b6dd3624949ef
Report timestampTue Nov 13 09:35:50 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/be9adfa40f58b4dfd03b6dd3624949ef.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 20}
include: [base_teaser.yaml]
meta_timestamp: 1542097002.226988
report: {name: be9adfa40f58b4dfd03b6dd3624949ef}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    be9adfa40f58b4dfd03b6dd3624949ef: {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 'D_melanogaster.fasta', title: !!python/unicode 'D_melanogaster',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie, bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[09:16:43] [Main        ] framework cmd:  ./teaser.py setups_generated/be9adfa40f58b4dfd03b6dd3624949ef.yaml -mcpu
[09:16:43] [Main        ] framework hash: vevev
[09:16:43] [Main        ] deployment mode: devel (True)
[09:16:43] [Main        ] Test Runner Setup - ""

[09:16:44] [Main        ] Using Teaser for data set creation
[09:16:44] [Teaser      ] Init. Creating 1 test datasets.
[09:16:44] [Teaser      ] 
[09:16:44] [Teaser      ] Creating test be9adfa40f58b4dfd03b6dd3624949ef
[09:16:44] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef
[09:16:44] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef
[09:16:44] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[09:16:44] [Teaser      ] csample /project/teaser/genometeaser/references/D_melanogaster.fasta 400 0.250000
[09:16:44] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[09:16:44] [Teaser      ] Sampling as contig: 89828 regions of size 400 (pad 80), totalling 35931498 base pairs
[09:16:44] [Teaser      ] Sampling 89828 regions
[09:17:11] [Teaser      ] 10%
[09:17:20] [Teaser      ] 20%
[09:17:28] [Teaser      ] 30%
[09:17:37] [Teaser      ] 40%
[09:17:46] [Teaser      ] 50%
[09:17:55] [Teaser      ] 60%
[09:18:03] [Teaser      ] 70%
[09:18:13] [Teaser      ] 80%
[09:18:27] [Teaser      ] 90%
[09:18:47] [Teaser      ] 100%
[09:18:50] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef
[09:18:50] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 40 -N 898287  --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.4.400.80.fasta
[09:18:50] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 40 -N 898287  --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.4.400.80.fasta
[09:20:30] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.400.80.fasta.fastq -> ./reads.fastq
[09:20:30] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.400.80.fasta.fastq.sam -> ./mapping_comparison.sam
[09:20:30] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef
[09:20:30] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[09:20:30] [Teaser      ] Translating SAM file coordinates (as contig)...
[09:20:30] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[09:21:54] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.400.80.fasta
[09:21:54] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.400.80.fasta.index
[09:21:55] [Teaser      ] remove mapping_comparison_unfixed.sam
[09:21:55] [Teaser      ] Took 310 seconds for generating be9adfa40f58b4dfd03b6dd3624949ef
[09:21:55] [Main        ] Data set creation completed
[09:21:55] [Main        ] 
[09:21:55] [bowtie      ] be9adfa40f58b4dfd03b6dd3624949ef (base: tests_base/base_mapping)
[09:21:55] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[09:21:55] [init        ] Reads: /project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef/reads.fastq
[09:21:55] [init        ] Output:/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef/out_bowtie.sam
[09:21:55] [map         ] Command(pre): 
[09:21:55] [map         ] Base run time file not existing, performing base run
[09:21:56] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie --threads 4  -S /project/teaser/genometeaser/references/D_melanogaster.fasta_bo reads_base.fastq out_bowtie.sam
[09:22:09] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie --threads 4  -S /project/teaser/genometeaser/references/D_melanogaster.fasta_bo reads.fastq out_bowtie.sam
[09:22:09] [map         ]    Mapping 89.00MB to 146.00MB with bowtie...
[09:22:31] [map         ]    Took 21.855 (wall), 39.420 (CPU) seconds, initialization time: 0.599 (wall), 0.520 (CPU) seconds.
[09:22:31] [map         ] Command(post): 
[09:22:31] [sort_prepare] Sorting...
[09:23:25] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[09:24:07] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
723662,109869,64756,0,0,898287,1,0,0.868188465696,0.91786590362,0.892336318836

[09:24:08] [bowtie2     ] be9adfa40f58b4dfd03b6dd3624949ef (base: tests_base/base_mapping)
[09:24:08] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[09:24:08] [init        ] Reads: /project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef/reads.fastq
[09:24:08] [init        ] Output:/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef/out_bowtie2.sam
[09:24:08] [map         ] Command(pre): 
[09:24:08] [map         ] Base run time file not existing, performing base run
[09:24:08] [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
[09:24:25] [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
[09:24:25] [map         ]    Mapping 89.00MB to 146.00MB with bowtie2...
[09:24:55] [map         ]    Took 29.565 (wall), 66.492 (CPU) seconds, initialization time: 0.559 (wall), 0.612 (CPU) seconds.
[09:24:55] [map         ] Command(post): 
[09:24:55] [sort_prepare] Sorting...
[09:25:28] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[09:26:02] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
764491,114610,19186,0,0,898287,0,0,0.869628176967,0.97551797488,0.919534658265

[09:26:02] [bwa         ] be9adfa40f58b4dfd03b6dd3624949ef (base: tests_base/base_mapping)
[09:26:02] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[09:26:02] [init        ] Reads: /project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef/reads.fastq
[09:26:02] [init        ] Output:/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef/out_bwa.sam
[09:26:02] [map         ] Command(pre): 
[09:26:02] [map         ] Base run time file not existing, performing base run
[09:26:02] [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
[09:26:29] [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
[09:26:29] [map         ]    Mapping 89.00MB to 146.00MB with bwa...
[09:27:36] [map         ]    Took 65.074 (wall), 116.188 (CPU) seconds, initialization time: 0.598 (wall), 0.432 (CPU) seconds.
[09:27:36] [map         ] Command(post): 
[09:27:37] [sort_prepare] Sorting...
[09:28:09] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[09:29:09] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
776490,116317,5480,0,0,898287,0,0,0.869717643343,0.992992058519,0.927275691032

[09:29:09] [bwamem      ] be9adfa40f58b4dfd03b6dd3624949ef (base: tests_base/base_mapping)
[09:29:09] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[09:29:09] [init        ] Reads: /project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef/reads.fastq
[09:29:09] [init        ] Output:/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef/out_bwamem.sam
[09:29:09] [map         ] Command(pre): 
[09:29:09] [map         ] Base run time file not existing, performing base run
[09:29:09] [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
[09:29:11] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwamem.sam
[09:29:11] [map         ]    Mapping 89.00MB to 146.00MB with bwamem...
[09:29:49] [map         ]    Took 37.095 (wall), 90.648 (CPU) seconds, initialization time: 0.260 (wall), 0.180 (CPU) seconds.
[09:29:49] [map         ] Command(post): 
[09:29:49] [sort_prepare] Sorting...
[09:30:12] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[09:30:45] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
772185,115685,10417,0,0,898287,0,0,0.869705024384,0.986689275008,0.924511156128

[09:30:46] [bwasw       ] be9adfa40f58b4dfd03b6dd3624949ef (base: tests_base/base_mapping)
[09:30:46] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[09:30:46] [init        ] Reads: /project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef/reads.fastq
[09:30:46] [init        ] Output:/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef/out_bwasw.sam
[09:30:46] [map         ] Command(pre): 
[09:30:46] [map         ] Base run time file not existing, performing base run
[09:30:46] [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
[09:30:48] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwasw.sam
[09:30:48] [map         ]    Mapping 89.00MB to 146.00MB with bwasw...
[09:31:51] [map         ]    Took 62.805 (wall), 171.272 (CPU) seconds, initialization time: 0.366 (wall), 0.284 (CPU) seconds.
[09:31:51] [map         ] Command(post): 
[09:31:51] [sort_prepare] Sorting...
[09:32:14] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[09:32:56] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
660221,100503,137563,0,1,898287,0,0,0.867885067383,0.827568615064,0.847247495682

[09:32:56] [ngm         ] be9adfa40f58b4dfd03b6dd3624949ef (base: tests_base/base_mapping)
[09:32:56] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[09:32:56] [init        ] Reads: /project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef/reads.fastq
[09:32:56] [init        ] Output:/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef/out_ngm.sam
[09:32:56] [map         ] Command(pre): 
[09:32:56] [map         ] Base run time file not existing, performing base run
[09:32:57] [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
[09:33:58] [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
[09:33:58] [map         ]    Mapping 89.00MB to 146.00MB with ngm...
[09:34:34] [map         ]    Took 35.337 (wall), 57.064 (CPU) seconds, initialization time: 3.768 (wall), 3.932 (CPU) seconds.
[09:34:34] [map         ] Command(post): 
[09:34:34] [sort_prepare] Sorting...
[09:35:07] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 20)... 
[09:35:49] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
779685,115908,2694,0,0,898287,1,0,0.870579604798,0.996556656045,0.929318248457