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
E_coliE_coli5500
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 Accession4e92df353baa1274023a9524957cd99f
Report timestampSun Oct 21 22:57:14 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/4e92df353baa1274023a9524957cd99f.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1540155020.076531
report: {name: 4e92df353baa1274023a9524957cd99f}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    4e92df353baa1274023a9524957cd99f: {coverage: 1.0, error_rate_mult: 1.0, mutation_indel_avg_len: 10.0,
      mutation_indel_frac: 0.3, mutation_rate: 0.001, paired: false, platform: !!python/unicode 'illumina',
      read_length: 60, reference: !!python/unicode 'E_coli.fasta', title: !!python/unicode 'E_coli',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[22:50:22] [Main        ] framework cmd:  ./teaser.py setups_generated/4e92df353baa1274023a9524957cd99f.yaml -mcpu
[22:50:22] [Main        ] framework hash: vevev
[22:50:22] [Main        ] deployment mode: devel (True)
[22:50:22] [Main        ] Test Runner Setup - ""

[22:50:22] [Main        ] Using Teaser for data set creation
[22:50:23] [Teaser      ] Init. Creating 1 test datasets.
[22:50:23] [Teaser      ] 
[22:50:23] [Teaser      ] Creating test 4e92df353baa1274023a9524957cd99f
[22:50:23] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f
[22:50:23] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f
[22:50:23] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/E_coli.fasta.teaser.findex
[22:50:23] [Teaser      ] csample /project/teaser/genometeaser/references/E_coli.fasta 600 0.500000
[22:50:23] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/E_coli.fasta.teaser.findex
[22:50:23] [Teaser      ] Sampling as contig: 4276 regions of size 600 (pad 120), totalling 2566034 base pairs
[22:50:23] [Teaser      ] Sampling 4276 regions
[22:50:24] [Teaser      ] 10%
[22:50:24] [Teaser      ] 20%
[22:50:25] [Teaser      ] 30%
[22:50:25] [Teaser      ] 40%
[22:50:25] [Teaser      ] 50%
[22:50:26] [Teaser      ] 60%
[22:50:26] [Teaser      ] 70%
[22:50:27] [Teaser      ] 80%
[22:50:27] [Teaser      ] 90%
[22:50:28] [Teaser      ] 100%
[22:50:28] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f
[22:50:28] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 250000  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 22 --source-no-N  /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.600.120.fasta
[22:50:28] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 250000  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 22 --source-no-N  /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.600.120.fasta
[22:51:31] [Teaser      ] move /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.600.120.fasta.fastq -> ./reads.fastq
[22:51:31] [Teaser      ] move /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.600.120.fasta.fastq.sam -> ./mapping_comparison.sam
[22:51:31] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f
[22:51:31] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[22:51:31] [Teaser      ] Translating SAM file coordinates (as contig)...
[22:51:31] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/E_coli.fasta.teaser.findex
[22:52:05] [Teaser      ] remove /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.600.120.fasta
[22:52:05] [Teaser      ] remove /project/teaser/genometeaser/references/E_coli.fasta.sampled.2.600.120.fasta.index
[22:52:05] [Teaser      ] remove mapping_comparison_unfixed.sam
[22:52:05] [Teaser      ] Took 102 seconds for generating 4e92df353baa1274023a9524957cd99f
[22:52:06] [Main        ] Data set creation completed
[22:52:06] [Main        ] 
[22:52:07] [bowtie2     ] 4e92df353baa1274023a9524957cd99f (base: tests_base/base_mapping)
[22:52:08] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[22:52:08] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f/reads.fastq
[22:52:08] [init        ] Output:/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f/out_bowtie2.sam
[22:52:08] [map         ] Command(pre): 
[22:52:08] [map         ] Base run time file not existing, performing base run
[22:52:08] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
[22:52:12] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -U reads.fastq -S out_bowtie2.sam
[22:52:12] [map         ]    Mapping 35.00MB to 5.00MB with bowtie2...
[22:52:23] [map         ]    Took 10.591 (wall), 19.668 (CPU) seconds, initialization time: 0.338 (wall), 0.388 (CPU) seconds.
[22:52:23] [map         ] Command(post): 
[22:52:23] [sort_prepare] Sorting...
[22:52:44] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[22:53:06] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
238984,9575,1441,0,0,250000,0,0,0.961477958955,0.994006446917,0.977471655514

[22:53:06] [bwa         ] 4e92df353baa1274023a9524957cd99f (base: tests_base/base_mapping)
[22:53:06] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[22:53:06] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f/reads.fastq
[22:53:06] [init        ] Output:/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f/out_bwa.sam
[22:53:06] [map         ] Command(pre): 
[22:53:06] [map         ] Base run time file not existing, performing base run
[22:53:06] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/E_coli.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[22:53:09] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/E_coli.fasta reads.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/E_coli.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
[22:53:09] [map         ]    Mapping 35.00MB to 5.00MB with bwa...
[22:53:29] [map         ]    Took 18.352 (wall), 20.052 (CPU) seconds, initialization time: 0.157 (wall), 0.044 (CPU) seconds.
[22:53:29] [map         ] Command(post): 
[22:53:29] [sort_prepare] Sorting...
[22:53:38] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[22:53:59] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
236924,9526,3550,0,0,250000,0,0,0.961347129235,0.985237489292,0.973145706517

[22:54:00] [bwamem      ] 4e92df353baa1274023a9524957cd99f (base: tests_base/base_mapping)
[22:54:00] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[22:54:00] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f/reads.fastq
[22:54:00] [init        ] Output:/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f/out_bwamem.sam
[22:54:00] [map         ] Command(pre): 
[22:54:00] [map         ] Base run time file not existing, performing base run
[22:54:00] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq  -t 4 > out_bwamem.sam
[22:54:02] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads.fastq  -t 4 > out_bwamem.sam
[22:54:02] [map         ]    Mapping 35.00MB to 5.00MB with bwamem...
[22:54:11] [map         ]    Took 8.143 (wall), 11.200 (CPU) seconds, initialization time: 0.091 (wall), 0.032 (CPU) seconds.
[22:54:11] [map         ] Command(post): 
[22:54:11] [sort_prepare] Sorting...
[22:54:18] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[22:54:39] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
240286,9655,59,0,0,250000,0,0,0.961370883529,0.999754519545,0.980187074483

[22:54:39] [bwasw       ] 4e92df353baa1274023a9524957cd99f (base: tests_base/base_mapping)
[22:54:39] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[22:54:39] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f/reads.fastq
[22:54:39] [init        ] Output:/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f/out_bwasw.sam
[22:54:39] [map         ] Command(pre): 
[22:54:40] [map         ] Base run time file not existing, performing base run
[22:54:40] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq  -t 4 > out_bwasw.sam
[22:54:42] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads.fastq  -t 4 > out_bwasw.sam
[22:54:42] [map         ]    Mapping 35.00MB to 5.00MB with bwasw...
[22:55:21] [map         ]    Took 38.122 (wall), 75.124 (CPU) seconds, initialization time: 0.088 (wall), 0.036 (CPU) seconds.
[22:55:21] [map         ] Command(post): 
[22:55:21] [sort_prepare] Sorting...
[22:55:28] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[22:55:49] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
235905,9515,4580,0,21,250000,0,0,0.961229728628,0.980955153128,0.970992272152

[22:55:49] [ngm         ] 4e92df353baa1274023a9524957cd99f (base: tests_base/base_mapping)
[22:55:49] [init        ] Ref:   /project/teaser/genometeaser/references/E_coli.fasta
[22:55:49] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f/reads.fastq
[22:55:49] [init        ] Output:/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f/out_ngm.sam
[22:55:49] [map         ] Command(pre): 
[22:55:49] [map         ] Base run time file not existing, performing base run
[22:55:49] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/E_coli.fasta -t 4 --qry reads_base.fastq  --no-progress
[22:56:30] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/E_coli.fasta -t 4 --qry reads.fastq  --no-progress
[22:56:30] [map         ]    Mapping 35.00MB to 5.00MB with ngm...
[22:56:44] [map         ]    Took 13.530 (wall), 20.048 (CPU) seconds, initialization time: 3.036 (wall), 3.132 (CPU) seconds.
[22:56:44] [map         ] Command(post): 
[22:56:44] [sort_prepare] Sorting...
[22:56:52] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[22:57:13] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
240151,9817,32,0,0,250000,0,0,0.960726973053,0.999866768256,0.979906192173