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 Accession023be73dabd493f04945e37217bf7c31
Report timestampSat Nov 10 03:45:48 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/023be73dabd493f04945e37217bf7c31.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1541814245.090401
report: {name: 023be73dabd493f04945e37217bf7c31}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    023be73dabd493f04945e37217bf7c31: {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 '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
[02:44:07] [Main        ] framework cmd:  ./teaser.py setups_generated/023be73dabd493f04945e37217bf7c31.yaml -mcpu
[02:44:07] [Main        ] framework hash: vevev
[02:44:07] [Main        ] deployment mode: devel (True)
[02:44:07] [Main        ] Test Runner Setup - ""

[02:44:07] [Main        ] Using Teaser for data set creation
[02:44:07] [Teaser      ] Init. Creating 1 test datasets.
[02:44:08] [Teaser      ] 
[02:44:08] [Teaser      ] Creating test 023be73dabd493f04945e37217bf7c31
[02:44:08] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31
[02:44:08] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31
[02:44:08] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus.fasta.teaser.findex
[02:44:08] [Teaser      ] csample /project/teaser/genometeaser/references/M_musculus.fasta 600 0.010000
[02:44:08] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus.fasta.teaser.findex
[02:44:08] [Teaser      ] Sampling as contig: 80640 regions of size 600 (pad 120), totalling 48384255 base pairs
[02:44:08] [Teaser      ] Sampling 80640 regions
[02:52:29] [Teaser      ] 10%
[02:53:00] [Teaser      ] 20%
[02:53:19] [Teaser      ] 30%
[02:53:37] [Teaser      ] 40%
[02:53:54] [Teaser      ] 50%
[02:54:11] [Teaser      ] 60%
[02:54:29] [Teaser      ] 70%
[02:54:46] [Teaser      ] 80%
[02:55:03] [Teaser      ] 90%
[02:55:20] [Teaser      ] 100%
[02:55:23] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31
[02:55:23] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 806404  --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.100.600.120.fasta
[02:55:23] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 806404  --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.100.600.120.fasta
[02:57:37] [Teaser      ] move /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.600.120.fasta.fastq -> ./reads.fastq
[02:57:38] [Teaser      ] move /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.600.120.fasta.fastq.sam -> ./mapping_comparison.sam
[02:57:38] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31
[02:57:38] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[02:57:38] [Teaser      ] Translating SAM file coordinates (as contig)...
[02:57:38] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus.fasta.teaser.findex
[02:59:48] [Teaser      ] remove /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.600.120.fasta
[02:59:48] [Teaser      ] remove /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.600.120.fasta.index
[02:59:48] [Teaser      ] remove mapping_comparison_unfixed.sam
[02:59:48] [Teaser      ] Took 940 seconds for generating 023be73dabd493f04945e37217bf7c31
[02:59:48] [Main        ] Data set creation completed
[02:59:48] [Main        ] 
[02:59:50] [bowtie2     ] 023be73dabd493f04945e37217bf7c31 (base: tests_base/base_mapping)
[02:59:50] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[02:59:50] [init        ] Reads: /project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31/reads.fastq
[02:59:50] [init        ] Output:/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31/out_bowtie2.sam
[02:59:50] [map         ] Command(pre): 
[02:59:50] [map         ] Base run time file not existing, performing base run
[02:59:50] [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
[03:04:21] [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
[03:04:21] [map         ]    Mapping 112.00MB to 4919.00MB with bowtie2...
[03:05:57] [map         ]    Took 95.940 (wall), 366.692 (CPU) seconds, initialization time: 3.727 (wall), 3.752 (CPU) seconds.
[03:05:57] [map         ] Command(post): 
[03:05:57] [sort_prepare] Sorting...
[03:06:57] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[03:08:09] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
709556,93846,3002,0,0,806404,1,0,0.883189237766,0.995787009619,0.936114409351

[03:08:09] [bwa         ] 023be73dabd493f04945e37217bf7c31 (base: tests_base/base_mapping)
[03:08:09] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[03:08:09] [init        ] Reads: /project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31/reads.fastq
[03:08:09] [init        ] Output:/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31/out_bwa.sam
[03:08:09] [map         ] Command(pre): 
[03:08:09] [map         ] Base run time file not existing, performing base run
[03:08:09] [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
[03:20:28] [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
[03:20:28] [map         ]    Mapping 112.00MB to 4919.00MB with bwa...
[03:22:53] [map         ]    Took 144.788 (wall), 284.720 (CPU) seconds, initialization time: 12.439 (wall), 12.268 (CPU) seconds.
[03:22:53] [map         ] Command(post): 
[03:22:53] [sort_prepare] Sorting...
[03:23:25] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[03:24:36] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
705556,92885,7963,0,0,806404,1,0,0.883667046156,0.988839820664,0.933299822747

[03:24:36] [bwamem      ] 023be73dabd493f04945e37217bf7c31 (base: tests_base/base_mapping)
[03:24:36] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[03:24:36] [init        ] Reads: /project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31/reads.fastq
[03:24:36] [init        ] Output:/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31/out_bwamem.sam
[03:24:36] [map         ] Command(pre): 
[03:24:36] [map         ] Base run time file not existing, performing base run
[03:24:36] [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
[03:24:52] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq  -t 4 > out_bwamem.sam
[03:24:52] [map         ]    Mapping 112.00MB to 4919.00MB with bwamem...
[03:26:41] [map         ]    Took 108.306 (wall), 346.280 (CPU) seconds, initialization time: 7.650 (wall), 7.556 (CPU) seconds.
[03:26:41] [map         ] Command(post): 
[03:26:41] [sort_prepare] Sorting...
[03:27:08] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[03:28:18] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
713168,93083,153,0,0,806404,1,6,0.88454836025,0.99978551031,0.938643249547

[03:28:18] [bwasw       ] 023be73dabd493f04945e37217bf7c31 (base: tests_base/base_mapping)
[03:28:18] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[03:28:18] [init        ] Reads: /project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31/reads.fastq
[03:28:18] [init        ] Output:/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31/out_bwasw.sam
[03:28:18] [map         ] Command(pre): 
[03:28:18] [map         ] Base run time file not existing, performing base run
[03:28:18] [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
[03:28:34] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq  -t 4 > out_bwasw.sam
[03:28:34] [map         ]    Mapping 112.00MB to 4919.00MB with bwasw...
[03:31:09] [map         ]    Took 154.749 (wall), 422.092 (CPU) seconds, initialization time: 7.602 (wall), 7.512 (CPU) seconds.
[03:31:09] [map         ] Command(post): 
[03:31:09] [sort_prepare] Sorting...
[03:31:37] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[03:32:46] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
684714,93256,28434,0,67,806404,1,0,0.88012905382,0.960128893301,0.918390093876

[03:32:46] [ngm         ] 023be73dabd493f04945e37217bf7c31 (base: tests_base/base_mapping)
[03:32:46] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[03:32:46] [init        ] Reads: /project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31/reads.fastq
[03:32:46] [init        ] Output:/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31/out_ngm.sam
[03:32:46] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/M_musculus.fasta 
[03:42:12] [map         ] Base run time file not existing, performing base run
[03:42:12] [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
[03:42:38] [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
[03:42:38] [map         ]    Mapping 112.00MB to 4919.00MB with ngm...
[03:44:04] [map         ]    Took 85.572 (wall), 264.688 (CPU) seconds, initialization time: 10.398 (wall), 10.856 (CPU) seconds.
[03:44:04] [map         ] Command(post): 
[03:44:04] [sort_prepare] Sorting...
[03:44:38] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[03:45:48] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
707804,83329,15271,0,0,806404,1,0,0.894671313167,0.978880475746,0.934883450622