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
M_musculus_cutfM_musculus_cutf5500
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 Accessionef84d4ed82d0fef31ff0765d0f19324d
Report timestampSat Aug 19 09:16:04 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/ef84d4ed82d0fef31ff0765d0f19324d.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 50}
include: [base_teaser.yaml]
meta_timestamp: 1503105865.739783
report: {name: ef84d4ed82d0fef31ff0765d0f19324d}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    ef84d4ed82d0fef31ff0765d0f19324d: {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: 100, reference: !!python/unicode 'M_musculus_cutf.fasta', title: !!python/unicode 'M_musculus_cutf',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[03:24:28] [Main        ] framework cmd:  ./teaser.py setups_generated/ef84d4ed82d0fef31ff0765d0f19324d.yaml -mcpu
[03:24:28] [Main        ] framework hash: vevev
[03:24:28] [Main        ] deployment mode: devel (True)
[03:24:28] [Main        ] Test Runner Setup - ""

[03:24:28] [Main        ] Using Teaser for data set creation
[03:24:29] [Teaser      ] Init. Creating 1 test datasets.
[03:24:29] [Teaser      ] 
[03:24:29] [Teaser      ] Creating test ef84d4ed82d0fef31ff0765d0f19324d
[03:24:29] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d
[03:24:29] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d
[03:24:29] [Teaser      ] Indexing /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[03:32:39] [Teaser      ] csample /project/teaser/genometeaser/references/M_musculus_cutf.fasta 1000 0.010000
[03:32:39] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus_cutf.fasta.teaser.findex
[03:32:39] [Teaser      ] Sampling as contig: 27255 regions of size 1000 (pad 200), totalling 27255376 base pairs
[03:32:39] [Teaser      ] Sampling 27255 regions
[03:32:43] [Teaser      ] 10%
[03:32:46] [Teaser      ] 20%
[03:32:50] [Teaser      ] 30%
[03:32:53] [Teaser      ] 40%
[03:32:56] [Teaser      ] 50%
[03:33:01] [Teaser      ] 60%
[03:33:05] [Teaser      ] 70%
[03:33:08] [Teaser      ] 80%
[03:33:11] [Teaser      ] 90%
[03:33:15] [Teaser      ] 100%
[03:33:16] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d
[03:33:17] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 100 -N 272553  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/M_musculus_cutf.fasta.sampled.100.1000.200.fasta
[03:33:17] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 100 -N 272553  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/M_musculus_cutf.fasta.sampled.100.1000.200.fasta
[03:35:23] [Teaser      ] move /project/teaser/genometeaser/references/M_musculus_cutf.fasta.sampled.100.1000.200.fasta.fastq -> ./reads.fastq
[03:35:23] [Teaser      ] move /project/teaser/genometeaser/references/M_musculus_cutf.fasta.sampled.100.1000.200.fasta.fastq.sam -> ./mapping_comparison.sam
[03:35:23] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d
[03:35:23] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[03:35:23] [Teaser      ] Translating SAM file coordinates (as contig)...
[03:35:23] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus_cutf.fasta.teaser.findex
[03:36:06] [Teaser      ] remove /project/teaser/genometeaser/references/M_musculus_cutf.fasta.sampled.100.1000.200.fasta
[03:36:06] [Teaser      ] remove /project/teaser/genometeaser/references/M_musculus_cutf.fasta.sampled.100.1000.200.fasta.index
[03:36:06] [Teaser      ] remove mapping_comparison_unfixed.sam
[03:36:06] [Teaser      ] Took 697 seconds for generating ef84d4ed82d0fef31ff0765d0f19324d
[03:36:06] [Main        ] Data set creation completed
[03:36:06] [Main        ] 
[03:36:08] [bowtie2     ] ef84d4ed82d0fef31ff0765d0f19324d (base: tests_base/base_mapping)
[03:36:08] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[03:36:08] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d/reads.fastq
[03:36:08] [init        ] Output:/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d/out_bowtie2.sam
[03:36:08] [map         ] Command(pre): /project/teaser/genometeaser/software/bowtie2/bowtie2-build /project/teaser/genometeaser/references/M_musculus_cutf.fasta /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt
[07:26:19] [map         ] Base run time file not existing, performing base run
[07:26:20] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
[07:26:29] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads.fastq -S out_bowtie2.sam
[07:26:29] [map         ]    Mapping 59.00MB to 2770.00MB with bowtie2...
[07:27:41] [map         ]    Took 71.137 (wall), 264.260 (CPU) seconds, initialization time: 3.546 (wall), 3.592 (CPU) seconds.
[07:27:41] [map         ] Command(post): 
[07:27:41] [sort_prepare] Sorting...
[07:28:09] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[07:28:39] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
249783,22618,152,0,0,272553,0,0,0.916967999383,0.999391841879,0.956407369969

[07:28:40] [bwa         ] ef84d4ed82d0fef31ff0765d0f19324d (base: tests_base/base_mapping)
[07:28:40] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[07:28:40] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d/reads.fastq
[07:28:40] [init        ] Output:/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d/out_bwa.sam
[07:28:40] [map         ] Command(pre): /project/teaser/genometeaser/software/bwa index /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[08:46:57] [map         ] Base run time file not existing, performing base run
[08:46:57] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[08:47:15] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
[08:47:15] [map         ]    Mapping 59.00MB to 2770.00MB with bwa...
[08:48:48] [map         ]    Took 92.596 (wall), 233.932 (CPU) seconds, initialization time: 8.873 (wall), 8.692 (CPU) seconds.
[08:48:48] [map         ] Command(post): 
[08:48:48] [sort_prepare] Sorting...
[08:49:00] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[08:49:30] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
245537,21987,5029,0,0,272553,0,0,0.917812981265,0.979929439748,0.947854619854

[08:49:30] [bwamem      ] ef84d4ed82d0fef31ff0765d0f19324d (base: tests_base/base_mapping)
[08:49:30] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[08:49:30] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d/reads.fastq
[08:49:30] [init        ] Output:/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d/out_bwamem.sam
[08:49:30] [map         ] Command(pre): 
[08:49:30] [map         ] Base run time file not existing, performing base run
[08:49:31] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq  -t 4 > out_bwamem.sam
[08:49:42] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq  -t 4 > out_bwamem.sam
[08:49:42] [map         ]    Mapping 59.00MB to 2770.00MB with bwamem...
[08:50:38] [map         ]    Took 55.811 (wall), 175.756 (CPU) seconds, initialization time: 4.581 (wall), 4.456 (CPU) seconds.
[08:50:38] [map         ] Command(post): 
[08:50:38] [sort_prepare] Sorting...
[08:50:50] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[08:51:18] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
250531,22022,0,0,0,272553,0,5,0.919201036129,1.0,0.95789968724

[08:51:18] [bwasw       ] ef84d4ed82d0fef31ff0765d0f19324d (base: tests_base/base_mapping)
[08:51:18] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[08:51:18] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d/reads.fastq
[08:51:18] [init        ] Output:/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d/out_bwasw.sam
[08:51:18] [map         ] Command(pre): 
[08:51:18] [map         ] Base run time file not existing, performing base run
[08:51:18] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq  -t 4 > out_bwasw.sam
[08:51:30] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq  -t 4 > out_bwasw.sam
[08:51:30] [map         ]    Mapping 59.00MB to 2770.00MB with bwasw...
[08:53:09] [map         ]    Took 98.186 (wall), 339.700 (CPU) seconds, initialization time: 4.595 (wall), 4.492 (CPU) seconds.
[08:53:09] [map         ] Command(post): 
[08:53:09] [sort_prepare] Sorting...
[08:53:19] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[08:53:47] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
249521,22619,413,0,26,272553,0,0,0.916884691703,0.998347563757,0.955883648678

[08:53:47] [ngm         ] ef84d4ed82d0fef31ff0765d0f19324d (base: tests_base/base_mapping)
[08:53:47] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[08:53:47] [init        ] Reads: /project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d/reads.fastq
[08:53:47] [init        ] Output:/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d/out_ngm.sam
[08:53:47] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/M_musculus_cutf.fasta 
[09:13:35] [map         ] Base run time file not existing, performing base run
[09:13:35] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/M_musculus_cutf.fasta -t 4 --qry reads_base.fastq  --no-progress
[09:14:14] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/M_musculus_cutf.fasta -t 4 --qry reads.fastq  --no-progress
[09:14:14] [map         ]    Mapping 59.00MB to 2770.00MB with ngm...
[09:15:23] [map         ]    Took 68.806 (wall), 181.376 (CPU) seconds, initialization time: 16.944 (wall), 24.000 (CPU) seconds.
[09:15:23] [map         ] Command(post): 
[09:15:23] [sort_prepare] Sorting...
[09:15:34] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[09:16:04] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
249020,21165,2368,0,0,272553,0,0,0.92166478524,0.990580298184,0.954880716602