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 Accession0bc744fc434e081e5d0279784d2334f3
Report timestampSat Aug 19 01:09:01 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/0bc744fc434e081e5d0279784d2334f3.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1503096324.638441
report: {name: 0bc744fc434e081e5d0279784d2334f3}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    0bc744fc434e081e5d0279784d2334f3: {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: 60, 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
[00:45:26] [Main        ] framework cmd:  ./teaser.py setups_generated/0bc744fc434e081e5d0279784d2334f3.yaml -mcpu
[00:45:26] [Main        ] framework hash: vevev
[00:45:26] [Main        ] deployment mode: devel (True)
[00:45:26] [Main        ] Test Runner Setup - ""

[00:45:26] [Main        ] Using Teaser for data set creation
[00:45:27] [Teaser      ] Init. Creating 1 test datasets.
[00:45:27] [Teaser      ] 
[00:45:27] [Teaser      ] Creating test 0bc744fc434e081e5d0279784d2334f3
[00:45:27] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3
[00:45:27] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3
[00:45:27] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[00:45:27] [Teaser      ] csample /project/teaser/genometeaser/references/D_melanogaster.fasta 600 0.250000
[00:45:27] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[00:45:27] [Teaser      ] Sampling as contig: 59885 regions of size 600 (pad 120), totalling 35931498 base pairs
[00:45:27] [Teaser      ] Sampling 59885 regions
[00:45:54] [Teaser      ] 10%
[00:46:07] [Teaser      ] 20%
[00:46:21] [Teaser      ] 30%
[00:46:32] [Teaser      ] 40%
[00:46:41] [Teaser      ] 50%
[00:46:50] [Teaser      ] 60%
[00:47:05] [Teaser      ] 70%
[00:47:19] [Teaser      ] 80%
[00:47:35] [Teaser      ] 90%
[00:47:51] [Teaser      ] 100%
[00:47:54] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3
[00:47:54] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 598858  --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.4.600.120.fasta
[00:47:54] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 598858  --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.4.600.120.fasta
[00:50:41] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq -> ./reads.fastq
[00:50:41] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq.sam -> ./mapping_comparison.sam
[00:50:41] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3
[00:50:41] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[00:50:41] [Teaser      ] Translating SAM file coordinates (as contig)...
[00:50:41] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[00:52:27] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta
[00:52:27] [Teaser      ] remove /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.index
[00:52:27] [Teaser      ] remove mapping_comparison_unfixed.sam
[00:52:27] [Teaser      ] Took 420 seconds for generating 0bc744fc434e081e5d0279784d2334f3
[00:52:27] [Main        ] Data set creation completed
[00:52:27] [Main        ] 
[00:52:29] [bowtie2     ] 0bc744fc434e081e5d0279784d2334f3 (base: tests_base/base_mapping)
[00:52:29] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[00:52:29] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3/reads.fastq
[00:52:29] [init        ] Output:/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3/out_bowtie2.sam
[00:52:29] [map         ] Command(pre): 
[00:52:29] [map         ] Base run time file not existing, performing base run
[00:52:29] [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
[00:52:47] [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
[00:52:47] [map         ]    Mapping 83.00MB to 146.00MB with bowtie2...
[00:53:26] [map         ]    Took 37.956 (wall), 99.388 (CPU) seconds, initialization time: 1.866 (wall), 1.820 (CPU) seconds.
[00:53:26] [map         ] Command(post): 
[00:53:26] [sort_prepare] Sorting...
[00:54:24] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[00:55:24] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
527971,68963,1924,0,0,598858,0,0,0.884471315087,0.99636909199,0.937091608398

[00:55:24] [bwa         ] 0bc744fc434e081e5d0279784d2334f3 (base: tests_base/base_mapping)
[00:55:24] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[00:55:24] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3/reads.fastq
[00:55:24] [init        ] Output:/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3/out_bwa.sam
[00:55:24] [map         ] Command(pre): 
[00:55:24] [map         ] Base run time file not existing, performing base run
[00:55:24] [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
[00:55:52] [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
[00:55:52] [map         ]    Mapping 83.00MB to 146.00MB with bwa...
[00:57:10] [map         ]    Took 77.036 (wall), 165.164 (CPU) seconds, initialization time: 3.882 (wall), 3.724 (CPU) seconds.
[00:57:10] [map         ] Command(post): 
[00:57:11] [sort_prepare] Sorting...
[00:57:32] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[00:58:32] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
524499,68084,6275,0,0,598858,0,0,0.88510639016,0.988177642462,0.933806439093

[00:58:32] [bwamem      ] 0bc744fc434e081e5d0279784d2334f3 (base: tests_base/base_mapping)
[00:58:32] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[00:58:32] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3/reads.fastq
[00:58:32] [init        ] Output:/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3/out_bwamem.sam
[00:58:32] [map         ] Command(pre): 
[00:58:32] [map         ] Base run time file not existing, performing base run
[00:58:32] [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
[00:58:39] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwamem.sam
[00:58:39] [map         ]    Mapping 83.00MB to 146.00MB with bwamem...
[00:59:23] [map         ]    Took 43.426 (wall), 116.292 (CPU) seconds, initialization time: 2.553 (wall), 2.496 (CPU) seconds.
[00:59:23] [map         ] Command(post): 
[00:59:23] [sort_prepare] Sorting...
[00:59:47] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[01:00:53] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
529778,68983,97,0,0,598858,0,0,0.884790425562,0.999816937957,0.938793375366

[01:00:53] [bwasw       ] 0bc744fc434e081e5d0279784d2334f3 (base: tests_base/base_mapping)
[01:00:53] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[01:00:53] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3/reads.fastq
[01:00:53] [init        ] Output:/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3/out_bwasw.sam
[01:00:53] [map         ] Command(pre): 
[01:00:53] [map         ] Base run time file not existing, performing base run
[01:00:53] [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
[01:00:59] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq  -t 4 > out_bwasw.sam
[01:00:59] [map         ]    Mapping 83.00MB to 146.00MB with bwasw...
[01:03:21] [map         ]    Took 141.757 (wall), 384.676 (CPU) seconds, initialization time: 2.854 (wall), 2.728 (CPU) seconds.
[01:03:21] [map         ] Command(post): 
[01:03:22] [sort_prepare] Sorting...
[01:03:40] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[01:04:44] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
515433,68178,15247,0,28,598858,0,0,0.883179035351,0.971268937966,0.925131765401

[01:04:44] [ngm         ] 0bc744fc434e081e5d0279784d2334f3 (base: tests_base/base_mapping)
[01:04:44] [init        ] Ref:   /project/teaser/genometeaser/references/D_melanogaster.fasta
[01:04:44] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3/reads.fastq
[01:04:44] [init        ] Output:/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3/out_ngm.sam
[01:04:44] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/D_melanogaster.fasta 
[01:05:41] [map         ] Base run time file not existing, performing base run
[01:05:41] [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
[01:06:18] [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
[01:06:18] [map         ]    Mapping 83.00MB to 146.00MB with ngm...
[01:07:25] [map         ]    Took 66.673 (wall), 111.548 (CPU) seconds, initialization time: 16.842 (wall), 24.532 (CPU) seconds.
[01:07:25] [map         ] Command(post): 
[01:07:25] [sort_prepare] Sorting...
[01:07:54] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[01:09:00] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
529707,68505,646,0,0,598858,0,0,0.88548374155,0.998781943347,0.938726613