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
Saccharomyces_cerevisiaeSaccharomyces_cerevisiae5500
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 Accessionccbbfa15c14aa12f9ad8363903f909c3
Report timestampWed Oct 3 16:46:48 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/ccbbfa15c14aa12f9ad8363903f909c3.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 75}
include: [base_teaser.yaml]
meta_timestamp: 1538577407.063202
report: {name: ccbbfa15c14aa12f9ad8363903f909c3}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    ccbbfa15c14aa12f9ad8363903f909c3: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 400,
      insert_size_error: 50, mutation_indel_avg_len: 1.0, mutation_indel_frac: 0.3,
      mutation_rate: 0.02, paired: true, platform: !!python/unicode 'illumina', read_length: 150,
      reference: !!python/unicode 'Saccharomyces_cerevisiae.fasta', title: !!python/unicode 'Saccharomyces_cerevisiae',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[16:38:02] [Main        ] framework cmd:  ./teaser.py setups_generated/ccbbfa15c14aa12f9ad8363903f909c3.yaml -mcpu
[16:38:02] [Main        ] framework hash: vevev
[16:38:02] [Main        ] deployment mode: devel (True)
[16:38:02] [Main        ] Test Runner Setup - ""

[16:38:05] [Main        ] Using Teaser for data set creation
[16:38:19] [Teaser      ] Init. Creating 1 test datasets.
[16:38:20] [Teaser      ] 
[16:38:20] [Teaser      ] Creating test ccbbfa15c14aa12f9ad8363903f909c3
[16:38:21] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3
[16:38:21] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3
[16:38:22] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[16:38:22] [Teaser      ] csample /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 4500 0.500000
[16:38:22] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[16:38:22] [Teaser      ] Sampling as contig: 1350 regions of size 4500 (pad 900), totalling 6078552 base pairs
[16:38:23] [Teaser      ] Sampling 1350 regions
[16:38:23] [Teaser      ] 10%
[16:38:24] [Teaser      ] 20%
[16:38:24] [Teaser      ] 30%
[16:38:24] [Teaser      ] 40%
[16:38:24] [Teaser      ] 50%
[16:38:24] [Teaser      ] 60%
[16:38:24] [Teaser      ] 70%
[16:38:24] [Teaser      ] 80%
[16:38:25] [Teaser      ] 90%
[16:38:25] [Teaser      ] 100%
[16:38:28] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3
[16:38:28] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 50000 --mp  --ll 400 --le 50  --hi 0.006000  --hs 0.014000  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta
[16:38:28] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 50000 --mp  --ll 400 --le 50  --hi 0.006000  --hs 0.014000  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta
[16:39:29] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta_1.fastq -> ./reads1.fastq
[16:39:30] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta_2.fastq -> ./reads2.fastq
[16:39:31] [Teaser      ] move /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta.fastq.sam -> ./mapping_comparison.sam
[16:39:32] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3
[16:39:32] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[16:39:34] [Teaser      ] Translating SAM file coordinates (as contig)...
[16:39:35] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.teaser.findex
[16:39:53] [Teaser      ] remove /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta
[16:39:54] [Teaser      ] remove /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.sampled.2.4500.900.fasta.index
[16:39:55] [Teaser      ] remove mapping_comparison_unfixed.sam
[16:39:55] [Teaser      ] Took 96 seconds for generating ccbbfa15c14aa12f9ad8363903f909c3
[16:39:58] [Main        ] Data set creation completed
[16:39:58] [Main        ] 
[16:40:16] [bowtie2     ] ccbbfa15c14aa12f9ad8363903f909c3 (base: tests_base/base_mapping)
[16:40:21] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[16:40:21] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3/reads1.fastq
[16:40:21] [init        ] Output:/project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3/out_bowtie2.sam
[16:40:24] [map         ] Command(pre): 
[16:40:24] [map         ] Base run time file not existing, performing base run
[16:40:25] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
[16:40:31] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
[16:40:31] [map         ]    Mapping 32.00MB to 12.00MB with bowtie2...
[16:40:47] [map         ]    Took 15.216 (wall), 35.316 (CPU) seconds, initialization time: 0.410 (wall), 0.440 (CPU) seconds.
[16:40:47] [map         ] Command(post): 
[16:40:47] [sort_prepare] Sorting...
[16:41:02] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:41:15] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
99032,767,201,0,0,100000,0,0,0.99231455225,0.99797446414,0.995136460469

[16:41:15] [bwa         ] ccbbfa15c14aa12f9ad8363903f909c3 (base: tests_base/base_mapping)
[16:41:15] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[16:41:15] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3/reads1.fastq
[16:41:15] [init        ] Output:/project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3/out_bwa.sam
[16:41:15] [map         ] Command(pre): 
[16:41:15] [map         ] Base run time file not existing, performing base run
[16:41:15] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[16:41:23] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq  -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads2.fastq  -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
[16:41:23] [map         ]    Mapping 32.00MB to 12.00MB with bwa...
[16:42:04] [map         ]    Took 38.902 (wall), 50.256 (CPU) seconds, initialization time: 0.144 (wall), 0.064 (CPU) seconds.
[16:42:04] [map         ] Command(post): 
[16:42:05] [sort_prepare] Sorting...
[16:42:14] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:42:21] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
88410,572,11018,0,0,100000,0,0,0.993571733609,0.889186144748,0.938485218407

[16:42:26] [bwamem      ] ccbbfa15c14aa12f9ad8363903f909c3 (base: tests_base/base_mapping)
[16:42:28] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[16:42:28] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3/reads1.fastq
[16:42:28] [init        ] Output:/project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3/out_bwamem.sam
[16:42:29] [map         ] Command(pre): 
[16:42:30] [map         ] Base run time file not existing, performing base run
[16:42:31] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq  -t 4 > out_bwamem.sam
[16:42:47] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq  -t 4 > out_bwamem.sam
[16:42:48] [map         ]    Mapping 32.00MB to 12.00MB with bwamem...
[16:43:05] [map         ]    Took 16.050 (wall), 22.264 (CPU) seconds, initialization time: 6.297 (wall), 0.052 (CPU) seconds.
[16:43:05] [map         ] Command(post): 
[16:43:07] [sort_prepare] Sorting...
[16:43:16] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:43:31] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
99170,830,0,0,0,100000,0,0,0.9917,1.0,0.995832705729

[16:43:36] [bwasw       ] ccbbfa15c14aa12f9ad8363903f909c3 (base: tests_base/base_mapping)
[16:43:38] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[16:43:38] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3/reads1.fastq
[16:43:38] [init        ] Output:/project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3/out_bwasw.sam
[16:43:40] [map         ] Command(pre): 
[16:43:41] [map         ] Base run time file not existing, performing base run
[16:43:42] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq  -t 4 > out_bwasw.sam
[16:43:59] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads1.fastq reads2.fastq  -t 4 > out_bwasw.sam
[16:43:59] [map         ]    Mapping 32.00MB to 12.00MB with bwasw...
[16:44:50] [map         ]    Took 48.917 (wall), 90.320 (CPU) seconds, initialization time: 6.115 (wall), 0.052 (CPU) seconds.
[16:44:50] [map         ] Command(post): 
[16:44:52] [sort_prepare] Sorting...
[16:45:03] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:45:19] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
99090,910,0,0,1,100000,0,0,0.9909,1.0,0.995429202873

[16:45:23] [ngm         ] ccbbfa15c14aa12f9ad8363903f909c3 (base: tests_base/base_mapping)
[16:45:26] [init        ] Ref:   /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta
[16:45:26] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3/reads1.fastq
[16:45:26] [init        ] Output:/project/teaser/genometeaser/tests_generated/ccbbfa15c14aa12f9ad8363903f909c3/out_ngm.sam
[16:45:28] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 
[16:45:37] [map         ] Base run time file not existing, performing base run
[16:45:38] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta -t 4 --qry reads_base.fastq  --no-progress
[16:46:01] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta -t 4  --no-progress
[16:46:01] [map         ]    Mapping 32.00MB to 12.00MB with ngm...
[16:46:24] [map         ]    Took 21.486 (wall), 18.252 (CPU) seconds, initialization time: 10.775 (wall), 3.124 (CPU) seconds.
[16:46:24] [map         ] Command(post): 
[16:46:26] [sort_prepare] Sorting...
[16:46:36] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[16:46:43] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
99091,909,0,0,0,100000,0,0,0.99091,1.0,0.99543424866