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.

6 tests executed, 0 fail, 0 aborted, 0 errors total.
StateNameReferenceExecutedOKWarningsErrors
H_sapiensH_sapiens6600
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 Accession4ff0769a44d529563c64b75a1aaf552d
Report timestampMon Aug 6 14:35:07 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/4ff0769a44d529563c64b75a1aaf552d.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 25}
include: [base_teaser.yaml]
meta_timestamp: 1533553427.934861
report: {name: 4ff0769a44d529563c64b75a1aaf552d}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    4ff0769a44d529563c64b75a1aaf552d: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 100,
      insert_size_error: 50, mutation_indel_avg_len: 1.0, mutation_indel_frac: 0.3,
      mutation_rate: 0.001, paired: true, platform: !!python/unicode 'illumina', read_length: 51,
      reference: !!python/unicode 'H_sapiens.fa', title: !!python/unicode 'H_sapiens',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: [bwamem_sec]
threads: 4
Log
[13:03:54] [Main        ] framework cmd:  ./teaser.py setups_generated/4ff0769a44d529563c64b75a1aaf552d.yaml -mcpu
[13:03:54] [Main        ] framework hash: vevev
[13:03:54] [Main        ] deployment mode: devel (True)
[13:03:54] [Main        ] Test Runner Setup - ""

[13:03:54] [Main        ] Using Teaser for data set creation
[13:03:55] [Teaser      ] Init. Creating 1 test datasets.
[13:03:55] [Teaser      ] 
[13:03:55] [Teaser      ] Creating test 4ff0769a44d529563c64b75a1aaf552d
[13:03:55] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d
[13:03:55] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d
[13:03:55] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[13:03:55] [Teaser      ] csample /project/teaser/genometeaser/references/H_sapiens.fa 1500 0.010000
[13:03:55] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[13:03:55] [Teaser      ] Sampling as contig: 20914 regions of size 1500 (pad 300), totalling 31371612 base pairs
[13:03:55] [Teaser      ] Sampling 20914 regions
[13:07:49] [Teaser      ] 10%
[13:09:46] [Teaser      ] 20%
[13:10:46] [Teaser      ] 30%
[13:11:12] [Teaser      ] 40%
[13:11:28] [Teaser      ] 50%
[13:11:39] [Teaser      ] 60%
[13:11:46] [Teaser      ] 70%
[13:11:53] [Teaser      ] 80%
[13:11:58] [Teaser      ] 90%
[13:12:03] [Teaser      ] 100%
[13:12:06] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d
[13:12:06] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 51 -N 307564 --mp  --ll 100 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta
[13:12:06] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 51 -N 307564 --mp  --ll 100 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta
[13:15:06] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta_1.fastq -> ./reads1.fastq
[13:15:06] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta_2.fastq -> ./reads2.fastq
[13:15:06] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta.fastq.sam -> ./mapping_comparison.sam
[13:15:06] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d
[13:15:06] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[13:15:06] [Teaser      ] Translating SAM file coordinates (as contig)...
[13:15:06] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[13:16:24] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta
[13:16:24] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta.index
[13:16:24] [Teaser      ] remove mapping_comparison_unfixed.sam
[13:16:24] [Teaser      ] Took 749 seconds for generating 4ff0769a44d529563c64b75a1aaf552d
[13:16:24] [Main        ] Data set creation completed
[13:16:24] [Main        ] 
[13:16:26] [bowtie2     ] 4ff0769a44d529563c64b75a1aaf552d (base: tests_base/base_mapping)
[13:16:27] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[13:16:27] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d/reads1.fastq
[13:16:27] [init        ] Output:/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d/out_bowtie2.sam
[13:16:27] [map         ] Command(pre): 
[13:16:27] [map         ] Base run time file not existing, performing base run
[13:16:27] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
[13:23:20] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
[13:23:20] [map         ]    Mapping 75.00MB to 3199.00MB with bowtie2...
[13:25:37] [map         ]    Took 135.573 (wall), 336.408 (CPU) seconds, initialization time: 37.304 (wall), 33.312 (CPU) seconds.
[13:25:37] [map         ] Command(post): 
[13:25:37] [sort_prepare] Sorting...
[13:26:43] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[13:27:32] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
588902,25238,988,0,0,615128,0,0,0.958905135637,0.998325111461,0.978218150711

[13:27:33] [bwa         ] 4ff0769a44d529563c64b75a1aaf552d (base: tests_base/base_mapping)
[13:27:33] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[13:27:33] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d/reads1.fastq
[13:27:33] [init        ] Output:/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d/out_bwa.sam
[13:27:33] [map         ] Command(pre): 
[13:27:33] [map         ] Base run time file not existing, performing base run
[13:27:33] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[13:39:01] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq  -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads2.fastq  -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
[13:39:01] [map         ]    Mapping 75.00MB to 3199.00MB with bwa...
[13:51:11] [map         ]    Took 729.492 (wall), 1127.316 (CPU) seconds, initialization time: 64.808 (wall), 59.812 (CPU) seconds.
[13:51:11] [map         ] Command(post): 
[13:51:12] [sort_prepare] Sorting...
[13:51:44] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[13:52:43] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
588343,25409,1376,0,0,615128,0,0,0.958600542239,0.99766668532,0.977743543467

[13:52:44] [bwamem      ] 4ff0769a44d529563c64b75a1aaf552d (base: tests_base/base_mapping)
[13:52:44] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[13:52:44] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d/reads1.fastq
[13:52:44] [init        ] Output:/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d/out_bwamem.sam
[13:52:44] [map         ] Command(pre): 
[13:52:44] [map         ] Base run time file not existing, performing base run
[13:52:44] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -t 4 > out_bwamem.sam
[13:53:56] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq  -t 4 > out_bwamem.sam
[13:53:56] [map         ]    Mapping 75.00MB to 3199.00MB with bwamem...
[14:01:18] [map         ]    Took 441.278 (wall), 729.752 (CPU) seconds, initialization time: 36.975 (wall), 33.696 (CPU) seconds.
[14:01:18] [map         ] Command(post): 
[14:01:18] [sort_prepare] Sorting...
[14:01:48] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:02:37] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
591761,23365,2,0,0,615128,0,1,0.962015912187,0.999996620269,0.980638650282

[14:02:37] [bwasw       ] 4ff0769a44d529563c64b75a1aaf552d (base: tests_base/base_mapping)
[14:02:37] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[14:02:37] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d/reads1.fastq
[14:02:37] [init        ] Output:/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d/out_bwasw.sam
[14:02:37] [map         ] Command(pre): 
[14:02:37] [map         ] Base run time file not existing, performing base run
[14:02:37] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -t 4 > out_bwasw.sam
[14:03:45] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq  -t 4 > out_bwasw.sam
[14:03:45] [map         ]    Mapping 75.00MB to 3199.00MB with bwasw...
[14:06:58] [map         ]    Took 191.925 (wall), 364.168 (CPU) seconds, initialization time: 29.302 (wall), 26.864 (CPU) seconds.
[14:06:58] [map         ] Command(post): 
[14:06:58] [sort_prepare] Sorting...
[14:07:24] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:08:15] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
573339,36023,5766,0,15,615128,0,0,0.940884072194,0.990043256404,0.964837896214

[14:08:15] [ngm         ] 4ff0769a44d529563c64b75a1aaf552d (base: tests_base/base_mapping)
[14:08:15] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[14:08:15] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d/reads1.fastq
[14:08:15] [init        ] Output:/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d/out_ngm.sam
[14:08:15] [map         ] Command(pre): 
[14:08:16] [map         ] Base run time file not existing, performing base run
[14:08:16] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq  --no-progress
[14:19:50] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4  --no-progress
[14:19:50] [map         ]    Mapping 75.00MB to 3199.00MB with ngm...
[14:22:28] [map         ]    Took 157.387 (wall), 329.744 (CPU) seconds, initialization time: 47.461 (wall), 49.424 (CPU) seconds.
[14:22:28] [map         ] Command(post): 
[14:22:28] [sort_prepare] Sorting...
[14:22:58] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:23:49] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
567314,37167,10645,2,0,615128,0,0,0.938514196476,0.981581738497,0.959564967356

[14:23:49] [bwamem_01   ] 4ff0769a44d529563c64b75a1aaf552d (base: tests_base/base_mapping)
[14:23:49] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[14:23:49] [init        ] Reads: /project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d/reads1.fastq
[14:23:49] [init        ] Output:/project/teaser/genometeaser/tests_generated/4ff0769a44d529563c64b75a1aaf552d/out_bwamem_01.sam
[14:23:49] [map         ] Command(pre): 
[14:23:49] [map         ] Base run time file not existing, performing base run
[14:23:49] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq  -M -t 4 > out_bwamem_01.sam
[14:24:45] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq  -M -t 4 > out_bwamem_01.sam
[14:24:45] [map         ]    Mapping 75.00MB to 3199.00MB with bwamem_01...
[14:33:53] [map         ]    Took 548.264 (wall), 962.304 (CPU) seconds, initialization time: 26.372 (wall), 25.756 (CPU) seconds.
[14:33:53] [map         ] Command(post): 
[14:33:53] [sort_prepare] Sorting...
[14:34:30] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 25)... 
[14:35:07] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
591761,23365,2,0,0,615128,0,1,0.962015912187,0.999996620269,0.980638650282