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
C_elegansC_elegans5500
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 Accession0b75acea7debea0665280a94869c22a6
Report timestampFri Jul 13 14:29:01 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/0b75acea7debea0665280a94869c22a6.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1531484135.442962
report: {name: 0b75acea7debea0665280a94869c22a6}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    0b75acea7debea0665280a94869c22a6: {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 'C_elegans.fa', title: !!python/unicode 'C_elegans',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[14:15:36] [Main        ] framework cmd:  ./teaser.py setups_generated/0b75acea7debea0665280a94869c22a6.yaml -mcpu
[14:15:36] [Main        ] framework hash: vevev
[14:15:36] [Main        ] deployment mode: devel (True)
[14:15:36] [Main        ] Test Runner Setup - ""

[14:15:37] [Main        ] Using Teaser for data set creation
[14:15:37] [Teaser      ] Init. Creating 1 test datasets.
[14:15:37] [Teaser      ] 
[14:15:37] [Teaser      ] Creating test 0b75acea7debea0665280a94869c22a6
[14:15:37] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6
[14:15:37] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6
[14:15:37] [Teaser      ] Indexing /project/teaser/genometeaser/references/C_elegans.fa
[14:15:57] [Teaser      ] csample /project/teaser/genometeaser/references/C_elegans.fa 600 0.250000
[14:15:57] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/C_elegans.fa.teaser.findex
[14:15:57] [Teaser      ] Sampling as contig: 41786 regions of size 600 (pad 120), totalling 25071600 base pairs
[14:15:58] [Teaser      ] Sampling 41786 regions
[14:16:01] [Teaser      ] 10%
[14:16:05] [Teaser      ] 20%
[14:16:09] [Teaser      ] 30%
[14:16:13] [Teaser      ] 40%
[14:16:17] [Teaser      ] 50%
[14:16:22] [Teaser      ] 60%
[14:16:27] [Teaser      ] 70%
[14:16:31] [Teaser      ] 80%
[14:16:36] [Teaser      ] 90%
[14:16:41] [Teaser      ] 100%
[14:16:43] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6
[14:16:43] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 417860  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/C_elegans.fa.sampled.4.600.120.fasta
[14:16:43] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 417860  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/C_elegans.fa.sampled.4.600.120.fasta
[14:18:29] [Teaser      ] move /project/teaser/genometeaser/references/C_elegans.fa.sampled.4.600.120.fasta.fastq -> ./reads.fastq
[14:18:29] [Teaser      ] move /project/teaser/genometeaser/references/C_elegans.fa.sampled.4.600.120.fasta.fastq.sam -> ./mapping_comparison.sam
[14:18:29] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6
[14:18:29] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[14:18:29] [Teaser      ] Translating SAM file coordinates (as contig)...
[14:18:29] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/C_elegans.fa.teaser.findex
[14:19:35] [Teaser      ] remove /project/teaser/genometeaser/references/C_elegans.fa.sampled.4.600.120.fasta
[14:19:35] [Teaser      ] remove /project/teaser/genometeaser/references/C_elegans.fa.sampled.4.600.120.fasta.index
[14:19:35] [Teaser      ] remove mapping_comparison_unfixed.sam
[14:19:35] [Teaser      ] Took 238 seconds for generating 0b75acea7debea0665280a94869c22a6
[14:19:36] [Main        ] Data set creation completed
[14:19:36] [Main        ] 
[14:19:37] [bowtie2     ] 0b75acea7debea0665280a94869c22a6 (base: tests_base/base_mapping)
[14:19:37] [init        ] Ref:   /project/teaser/genometeaser/references/C_elegans.fa
[14:19:37] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6/reads.fastq
[14:19:37] [init        ] Output:/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6/out_bowtie2.sam
[14:19:38] [map         ] Command(pre): 
[14:19:38] [map         ] Base run time file not existing, performing base run
[14:19:38] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/C_elegans.fa_bt -U reads_base.fastq -S out_bowtie2.sam
[14:19:51] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/C_elegans.fa_bt -U reads.fastq -S out_bowtie2.sam
[14:19:51] [map         ]    Mapping 58.00MB to 101.00MB with bowtie2...
[14:20:16] [map         ]    Took 24.579 (wall), 64.856 (CPU) seconds, initialization time: 0.498 (wall), 0.500 (CPU) seconds.
[14:20:16] [map         ] Command(post): 
[14:20:16] [sort_prepare] Sorting...
[14:20:49] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[14:21:26] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
399568,16992,1300,0,0,417860,1,0,0.959208757442,0.996757037229,0.977622493969

[14:21:26] [bwa         ] 0b75acea7debea0665280a94869c22a6 (base: tests_base/base_mapping)
[14:21:26] [init        ] Ref:   /project/teaser/genometeaser/references/C_elegans.fa
[14:21:26] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6/reads.fastq
[14:21:26] [init        ] Output:/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6/out_bwa.sam
[14:21:26] [map         ] Command(pre): 
[14:21:26] [map         ] Base run time file not existing, performing base run
[14:21:26] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/C_elegans.fa reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/C_elegans.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[14:21:44] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/C_elegans.fa reads.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/C_elegans.fa out_bwa.sam.bwa reads.fastq > out_bwa.sam
[14:21:44] [map         ]    Mapping 58.00MB to 101.00MB with bwa...
[14:22:26] [map         ]    Took 41.545 (wall), 73.200 (CPU) seconds, initialization time: 0.506 (wall), 0.264 (CPU) seconds.
[14:22:26] [map         ] Command(post): 
[14:22:26] [sort_prepare] Sorting...
[14:22:38] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[14:23:14] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
396860,16768,4232,0,0,417860,0,0,0.959461158336,0.989448804763,0.97422427337

[14:23:14] [bwamem      ] 0b75acea7debea0665280a94869c22a6 (base: tests_base/base_mapping)
[14:23:14] [init        ] Ref:   /project/teaser/genometeaser/references/C_elegans.fa
[14:23:14] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6/reads.fastq
[14:23:14] [init        ] Output:/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6/out_bwamem.sam
[14:23:14] [map         ] Command(pre): 
[14:23:15] [map         ] Base run time file not existing, performing base run
[14:23:15] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/C_elegans.fa reads_base.fastq  -t 4 > out_bwamem.sam
[14:23:17] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/C_elegans.fa reads.fastq  -t 4 > out_bwamem.sam
[14:23:17] [map         ]    Mapping 58.00MB to 101.00MB with bwamem...
[14:23:37] [map         ]    Took 19.095 (wall), 45.068 (CPU) seconds, initialization time: 0.213 (wall), 0.172 (CPU) seconds.
[14:23:37] [map         ] Command(post): 
[14:23:37] [sort_prepare] Sorting...
[14:23:47] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[14:24:23] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
400823,16981,56,0,0,417860,1,0,0.959356540387,0.999860306975,0.979189747436

[14:24:23] [bwasw       ] 0b75acea7debea0665280a94869c22a6 (base: tests_base/base_mapping)
[14:24:23] [init        ] Ref:   /project/teaser/genometeaser/references/C_elegans.fa
[14:24:23] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6/reads.fastq
[14:24:23] [init        ] Output:/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6/out_bwasw.sam
[14:24:23] [map         ] Command(pre): 
[14:24:23] [map         ] Base run time file not existing, performing base run
[14:24:23] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/C_elegans.fa reads_base.fastq  -t 4 > out_bwasw.sam
[14:24:25] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/C_elegans.fa reads.fastq  -t 4 > out_bwasw.sam
[14:24:25] [map         ]    Mapping 58.00MB to 101.00MB with bwasw...
[14:25:36] [map         ]    Took 70.610 (wall), 145.860 (CPU) seconds, initialization time: 0.220 (wall), 0.172 (CPU) seconds.
[14:25:36] [map         ] Command(post): 
[14:25:37] [sort_prepare] Sorting...
[14:25:47] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[14:26:23] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
389500,16809,11551,0,6,417860,0,0,0.958630008196,0.97119817679,0.964873166865

[14:26:23] [ngm         ] 0b75acea7debea0665280a94869c22a6 (base: tests_base/base_mapping)
[14:26:23] [init        ] Ref:   /project/teaser/genometeaser/references/C_elegans.fa
[14:26:23] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6/reads.fastq
[14:26:23] [init        ] Output:/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6/out_ngm.sam
[14:26:23] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/C_elegans.fa 
[14:27:39] [map         ] Base run time file not existing, performing base run
[14:27:39] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/C_elegans.fa -t 4 --qry reads_base.fastq  --no-progress
[14:27:51] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/C_elegans.fa -t 4 --qry reads.fastq  --no-progress
[14:27:51] [map         ]    Mapping 58.00MB to 101.00MB with ngm...
[14:28:13] [map         ]    Took 21.118 (wall), 35.356 (CPU) seconds, initialization time: 3.092 (wall), 3.240 (CPU) seconds.
[14:28:13] [map         ] Command(post): 
[14:28:13] [sort_prepare] Sorting...
[14:28:25] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[14:29:01] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
400351,17229,280,0,0,417860,1,0,0.958740840079,0.999301102511,0.978600874347