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
Bos_taurusBos_taurus5500
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 Accession14e5e97d9d3c2238f7310baab576d567
Report timestampWed Oct 3 17:04:39 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/14e5e97d9d3c2238f7310baab576d567.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 75}
include: [base_teaser.yaml]
meta_timestamp: 1538576629.063409
report: {name: 14e5e97d9d3c2238f7310baab576d567}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    14e5e97d9d3c2238f7310baab576d567: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 100,
      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: 150,
      reference: !!python/unicode 'Bos_taurus.fa', title: !!python/unicode 'Bos_taurus',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[16:23:52] [Main        ] framework cmd:  ./teaser.py setups_generated/14e5e97d9d3c2238f7310baab576d567.yaml -mcpu
[16:23:52] [Main        ] framework hash: vevev
[16:23:52] [Main        ] deployment mode: devel (True)
[16:23:52] [Main        ] Test Runner Setup - ""

[16:23:53] [Main        ] Using Teaser for data set creation
[16:23:53] [Teaser      ] Init. Creating 1 test datasets.
[16:23:53] [Teaser      ] 
[16:23:53] [Teaser      ] Creating test 14e5e97d9d3c2238f7310baab576d567
[16:23:53] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567
[16:23:53] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567
[16:23:53] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Bos_taurus.fa.teaser.findex
[16:23:53] [Teaser      ] csample /project/teaser/genometeaser/references/Bos_taurus.fa 1500 0.010000
[16:23:55] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Bos_taurus.fa.teaser.findex
[16:23:55] [Teaser      ] Sampling as contig: 17802 regions of size 1500 (pad 300), totalling 26704222 base pairs
[16:23:56] [Teaser      ] Sampling 17802 regions
[16:28:29] [Teaser      ] 10%
[16:30:06] [Teaser      ] 20%
[16:30:50] [Teaser      ] 30%
[16:31:16] [Teaser      ] 40%
[16:31:28] [Teaser      ] 50%
[16:31:35] [Teaser      ] 60%
[16:31:42] [Teaser      ] 70%
[16:31:49] [Teaser      ] 80%
[16:31:54] [Teaser      ] 90%
[16:31:59] [Teaser      ] 100%
[16:32:03] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567
[16:32:04] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 89014 --mp  --ll 100 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Bos_taurus.fa.sampled.100.1500.300.fasta
[16:32:04] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 89014 --mp  --ll 100 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Bos_taurus.fa.sampled.100.1500.300.fasta
[16:35:06] [Teaser      ] move /project/teaser/genometeaser/references/Bos_taurus.fa.sampled.100.1500.300.fasta_1.fastq -> ./reads1.fastq
[16:35:08] [Teaser      ] move /project/teaser/genometeaser/references/Bos_taurus.fa.sampled.100.1500.300.fasta_2.fastq -> ./reads2.fastq
[16:35:09] [Teaser      ] move /project/teaser/genometeaser/references/Bos_taurus.fa.sampled.100.1500.300.fasta.fastq.sam -> ./mapping_comparison.sam
[16:35:09] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567
[16:35:09] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[16:35:09] [Teaser      ] Translating SAM file coordinates (as contig)...
[16:35:09] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Bos_taurus.fa.teaser.findex
[16:35:44] [Teaser      ] remove /project/teaser/genometeaser/references/Bos_taurus.fa.sampled.100.1500.300.fasta
[16:35:44] [Teaser      ] remove /project/teaser/genometeaser/references/Bos_taurus.fa.sampled.100.1500.300.fasta.index
[16:35:44] [Teaser      ] remove mapping_comparison_unfixed.sam
[16:35:44] [Teaser      ] Took 711 seconds for generating 14e5e97d9d3c2238f7310baab576d567
[16:35:44] [Main        ] Data set creation completed
[16:35:44] [Main        ] 
[16:35:45] [bowtie2     ] 14e5e97d9d3c2238f7310baab576d567 (base: tests_base/base_mapping)
[16:35:45] [init        ] Ref:   /project/teaser/genometeaser/references/Bos_taurus.fa
[16:35:45] [init        ] Reads: /project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567/reads1.fastq
[16:35:45] [init        ] Output:/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567/out_bowtie2.sam
[16:35:45] [map         ] Command(pre): 
[16:35:45] [map         ] Base run time file not existing, performing base run
[16:35:45] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Bos_taurus.fa_bt -U reads_base.fastq -S out_bowtie2.sam
[16:40:32] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Bos_taurus.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
[16:40:32] [map         ]    Mapping 56.00MB to 2715.00MB with bowtie2...
[16:41:16] [map         ]    Took 41.910 (wall), 140.296 (CPU) seconds, initialization time: 2.981 (wall), 2.520 (CPU) seconds.
[16:41:16] [map         ] Command(post): 
[16:41:16] [sort_prepare] Sorting...
[16:41:33] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:41:43] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
174759,3223,46,0,0,178028,0,0,0.981891427223,0.999736849632,0.990733785542

[16:41:43] [bwa         ] 14e5e97d9d3c2238f7310baab576d567 (base: tests_base/base_mapping)
[16:41:43] [init        ] Ref:   /project/teaser/genometeaser/references/Bos_taurus.fa
[16:41:43] [init        ] Reads: /project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567/reads1.fastq
[16:41:43] [init        ] Output:/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567/out_bwa.sam
[16:41:43] [map         ] Command(pre): 
[16:41:43] [map         ] Base run time file not existing, performing base run
[16:41:44] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Bos_taurus.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[16:48:47] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Bos_taurus.fa reads1.fastq  -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Bos_taurus.fa reads2.fastq  -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Bos_taurus.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
[16:48:47] [map         ]    Mapping 56.00MB to 2715.00MB with bwa...
[16:50:54] [map         ]    Took 126.554 (wall), 344.412 (CPU) seconds, initialization time: 5.629 (wall), 5.500 (CPU) seconds.
[16:50:54] [map         ] Command(post): 
[16:50:54] [sort_prepare] Sorting...
[16:51:03] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:51:11] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
168731,2693,6604,0,0,178028,0,0,0.984290414411,0.962334958793,0.97318887181

[16:51:12] [bwamem      ] 14e5e97d9d3c2238f7310baab576d567 (base: tests_base/base_mapping)
[16:51:12] [init        ] Ref:   /project/teaser/genometeaser/references/Bos_taurus.fa
[16:51:12] [init        ] Reads: /project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567/reads1.fastq
[16:51:12] [init        ] Output:/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567/out_bwamem.sam
[16:51:12] [map         ] Command(pre): 
[16:51:12] [map         ] Base run time file not existing, performing base run
[16:51:12] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq  -t 4 > out_bwamem.sam
[16:51:22] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Bos_taurus.fa reads1.fastq reads2.fastq  -t 4 > out_bwamem.sam
[16:51:22] [map         ]    Mapping 56.00MB to 2715.00MB with bwamem...
[16:52:06] [map         ]    Took 43.977 (wall), 137.480 (CPU) seconds, initialization time: 5.895 (wall), 3.484 (CPU) seconds.
[16:52:06] [map         ] Command(post): 
[16:52:06] [sort_prepare] Sorting...
[16:52:15] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:52:34] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
176680,1348,0,0,0,178028,0,0,0.992428157369,1.0,0.996199691013

[16:52:42] [bwasw       ] 14e5e97d9d3c2238f7310baab576d567 (base: tests_base/base_mapping)
[16:52:42] [init        ] Ref:   /project/teaser/genometeaser/references/Bos_taurus.fa
[16:52:42] [init        ] Reads: /project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567/reads1.fastq
[16:52:42] [init        ] Output:/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567/out_bwasw.sam
[16:52:42] [map         ] Command(pre): 
[16:52:42] [map         ] Base run time file not existing, performing base run
[16:52:42] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq  -t 4 > out_bwasw.sam
[16:52:59] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Bos_taurus.fa reads1.fastq reads2.fastq  -t 4 > out_bwasw.sam
[16:52:59] [map         ]    Mapping 56.00MB to 2715.00MB with bwasw...
[16:54:47] [map         ]    Took 108.036 (wall), 385.172 (CPU) seconds, initialization time: 11.828 (wall), 4.216 (CPU) seconds.
[16:54:47] [map         ] Command(post): 
[16:54:47] [sort_prepare] Sorting...
[16:54:57] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:55:10] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
175201,2827,0,0,8,178028,0,0,0.984120475431,1.0,0.991996693363

[16:55:10] [ngm         ] 14e5e97d9d3c2238f7310baab576d567 (base: tests_base/base_mapping)
[16:55:10] [init        ] Ref:   /project/teaser/genometeaser/references/Bos_taurus.fa
[16:55:10] [init        ] Reads: /project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567/reads1.fastq
[16:55:10] [init        ] Output:/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567/out_ngm.sam
[16:55:10] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Bos_taurus.fa 
[17:03:06] [map         ] Base run time file not existing, performing base run
[17:03:06] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Bos_taurus.fa -t 4 --qry reads_base.fastq  --no-progress
[17:03:21] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/Bos_taurus.fa -t 4  --no-progress
[17:03:21] [map         ]    Mapping 56.00MB to 2715.00MB with ngm...
[17:04:10] [map         ]    Took 47.200 (wall), 94.744 (CPU) seconds, initialization time: 7.096 (wall), 7.224 (CPU) seconds.
[17:04:10] [map         ] Command(post): 
[17:04:10] [sort_prepare] Sorting...
[17:04:20] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[17:04:39] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
174325,3288,415,0,0,178028,0,0,0.981487841543,0.997625042921,0.98949065284