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_musculusM_musculus5500
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 Accession0c6bc0fb80fb6958e0d82aa8c71411b8
Report timestampSat Aug 19 02:58:18 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/0c6bc0fb80fb6958e0d82aa8c71411b8.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 50}
include: [base_teaser.yaml]
meta_timestamp: 1503099066.834774
report: {name: 0c6bc0fb80fb6958e0d82aa8c71411b8}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    0c6bc0fb80fb6958e0d82aa8c71411b8: {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.fasta', title: !!python/unicode 'M_musculus',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[01:31:09] [Main        ] framework cmd:  ./teaser.py setups_generated/0c6bc0fb80fb6958e0d82aa8c71411b8.yaml -mcpu
[01:31:09] [Main        ] framework hash: vevev
[01:31:09] [Main        ] deployment mode: devel (True)
[01:31:09] [Main        ] Test Runner Setup - ""

[01:31:09] [Main        ] Using Teaser for data set creation
[01:31:09] [Teaser      ] Init. Creating 1 test datasets.
[01:31:09] [Teaser      ] 
[01:31:09] [Teaser      ] Creating test 0c6bc0fb80fb6958e0d82aa8c71411b8
[01:31:09] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8
[01:31:09] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8
[01:31:09] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus.fasta.teaser.findex
[01:31:09] [Teaser      ] csample /project/teaser/genometeaser/references/M_musculus.fasta 1000 0.010000
[01:31:09] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus.fasta.teaser.findex
[01:31:09] [Teaser      ] Sampling as contig: 48384 regions of size 1000 (pad 200), totalling 48384255 base pairs
[01:31:09] [Teaser      ] Sampling 48384 regions
[01:38:16] [Teaser      ] 10%
[01:39:16] [Teaser      ] 20%
[01:39:37] [Teaser      ] 30%
[01:39:50] [Teaser      ] 40%
[01:40:04] [Teaser      ] 50%
[01:40:17] [Teaser      ] 60%
[01:40:30] [Teaser      ] 70%
[01:40:43] [Teaser      ] 80%
[01:40:56] [Teaser      ] 90%
[01:41:10] [Teaser      ] 100%
[01:41:12] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8
[01:41:12] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 100 -N 483842  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.1000.200.fasta
[01:41:12] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 100 -N 483842  --ll 500 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.1000.200.fasta
[01:46:01] [Teaser      ] move /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.1000.200.fasta.fastq -> ./reads.fastq
[01:46:01] [Teaser      ] move /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.1000.200.fasta.fastq.sam -> ./mapping_comparison.sam
[01:46:01] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8
[01:46:01] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[01:46:01] [Teaser      ] Translating SAM file coordinates (as contig)...
[01:46:01] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus.fasta.teaser.findex
[01:47:53] [Teaser      ] remove /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.1000.200.fasta
[01:47:54] [Teaser      ] remove /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.1000.200.fasta.index
[01:47:54] [Teaser      ] remove mapping_comparison_unfixed.sam
[01:47:54] [Teaser      ] Took 1004 seconds for generating 0c6bc0fb80fb6958e0d82aa8c71411b8
[01:47:54] [Main        ] Data set creation completed
[01:47:54] [Main        ] 
[01:47:55] [bowtie2     ] 0c6bc0fb80fb6958e0d82aa8c71411b8 (base: tests_base/base_mapping)
[01:47:55] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[01:47:55] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8/reads.fastq
[01:47:55] [init        ] Output:/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8/out_bowtie2.sam
[01:47:55] [map         ] Command(pre): 
[01:47:55] [map         ] Base run time file not existing, performing base run
[01:47:55] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
[01:52:53] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_bt -U reads.fastq -S out_bowtie2.sam
[01:52:53] [map         ]    Mapping 106.00MB to 4919.00MB with bowtie2...
[01:55:43] [map         ]    Took 168.617 (wall), 425.384 (CPU) seconds, initialization time: 30.529 (wall), 29.504 (CPU) seconds.
[01:55:43] [map         ] Command(post): 
[01:55:43] [sort_prepare] Sorting...
[01:56:28] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[01:57:28] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
442273,41297,272,0,0,483842,0,0,0.91459974771,0.999385373239,0.955114645589

[01:57:29] [bwa         ] 0c6bc0fb80fb6958e0d82aa8c71411b8 (base: tests_base/base_mapping)
[01:57:29] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[01:57:29] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8/reads.fastq
[01:57:29] [init        ] Output:/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8/out_bwa.sam
[01:57:29] [map         ] Command(pre): 
[01:57:29] [map         ] Base run time file not existing, performing base run
[01:57:29] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[02:11:50] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
[02:11:50] [map         ]    Mapping 106.00MB to 4919.00MB with bwa...
[02:19:24] [map         ]    Took 454.267 (wall), 924.712 (CPU) seconds, initialization time: 91.675 (wall), 90.532 (CPU) seconds.
[02:19:24] [map         ] Command(post): 
[02:19:24] [sort_prepare] Sorting...
[02:19:52] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[02:20:48] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
434777,40189,8876,0,0,483842,0,0,0.915385522332,0.979993373199,0.946588302659

[02:20:49] [bwamem      ] 0c6bc0fb80fb6958e0d82aa8c71411b8 (base: tests_base/base_mapping)
[02:20:49] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[02:20:49] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8/reads.fastq
[02:20:49] [init        ] Output:/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8/out_bwamem.sam
[02:20:49] [map         ] Command(pre): 
[02:20:49] [map         ] Base run time file not existing, performing base run
[02:20:49] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq  -t 4 > out_bwamem.sam
[02:24:02] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq  -t 4 > out_bwamem.sam
[02:24:02] [map         ]    Mapping 106.00MB to 4919.00MB with bwamem...
[02:29:29] [map         ]    Took 325.461 (wall), 769.492 (CPU) seconds, initialization time: 87.073 (wall), 84.256 (CPU) seconds.
[02:29:29] [map         ] Command(post): 
[02:29:29] [sort_prepare] Sorting...
[02:29:49] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[02:30:48] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
443656,40186,0,0,0,483842,0,4,0.916943961045,1.0,0.956672682852

[02:30:48] [bwasw       ] 0c6bc0fb80fb6958e0d82aa8c71411b8 (base: tests_base/base_mapping)
[02:30:48] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[02:30:48] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8/reads.fastq
[02:30:48] [init        ] Output:/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8/out_bwasw.sam
[02:30:48] [map         ] Command(pre): 
[02:30:48] [map         ] Base run time file not existing, performing base run
[02:30:48] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq  -t 4 > out_bwasw.sam
[02:33:25] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq  -t 4 > out_bwasw.sam
[02:33:25] [map         ]    Mapping 106.00MB to 4919.00MB with bwasw...
[02:40:19] [map         ]    Took 413.863 (wall), 1321.008 (CPU) seconds, initialization time: 78.563 (wall), 77.480 (CPU) seconds.
[02:40:19] [map         ] Command(post): 
[02:40:19] [sort_prepare] Sorting...
[02:40:42] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[02:41:34] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
441572,41517,753,0,36,483842,0,0,0.914059314122,0.998297631832,0.954323146181

[02:41:34] [ngm         ] 0c6bc0fb80fb6958e0d82aa8c71411b8 (base: tests_base/base_mapping)
[02:41:34] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[02:41:34] [init        ] Reads: /project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8/reads.fastq
[02:41:34] [init        ] Output:/project/teaser/genometeaser/tests_generated/0c6bc0fb80fb6958e0d82aa8c71411b8/out_ngm.sam
[02:41:34] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/M_musculus.fasta 
[02:51:08] [map         ] Base run time file not existing, performing base run
[02:51:08] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/M_musculus.fasta -t 4 --qry reads_base.fastq  --no-progress
[02:53:42] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/M_musculus.fasta -t 4 --qry reads.fastq  --no-progress
[02:53:42] [map         ]    Mapping 106.00MB to 4919.00MB with ngm...
[02:57:22] [map         ]    Took 219.545 (wall), 515.964 (CPU) seconds, initialization time: 78.648 (wall), 69.288 (CPU) seconds.
[02:57:22] [map         ] Command(post): 
[02:57:22] [sort_prepare] Sorting...
[02:57:44] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[02:58:18] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
441651,38258,3933,0,0,483842,0,0,0.920280719886,0.99117338145,0.954412405064