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
Gallus_gallusGallus_gallus5500
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 Accession42fc1d552498df3b8ed5a53dd70b689a
Report timestampThu Oct 11 01:21:24 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/42fc1d552498df3b8ed5a53dd70b689a.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 75}
include: [base_teaser.yaml]
meta_timestamp: 1539212658.350721
report: {name: 42fc1d552498df3b8ed5a53dd70b689a}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    42fc1d552498df3b8ed5a53dd70b689a: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 100,
      insert_size_error: 10, mutation_indel_avg_len: 1.0, mutation_indel_frac: 0.3,
      mutation_rate: 0.001, paired: true, platform: !!python/unicode 'illumina', read_length: 150,
      reference: !!python/unicode 'Gallus_gallus.fa', title: !!python/unicode 'Gallus_gallus',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[01:04:20] [Main        ] framework cmd:  ./teaser.py setups_generated/42fc1d552498df3b8ed5a53dd70b689a.yaml -mcpu
[01:04:20] [Main        ] framework hash: vevev
[01:04:20] [Main        ] deployment mode: devel (True)
[01:04:20] [Main        ] Test Runner Setup - ""

[01:04:21] [Main        ] Using Teaser for data set creation
[01:04:21] [Teaser      ] Init. Creating 1 test datasets.
[01:04:21] [Teaser      ] 
[01:04:21] [Teaser      ] Creating test 42fc1d552498df3b8ed5a53dd70b689a
[01:04:21] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a
[01:04:21] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a
[01:04:21] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Gallus_gallus.fa.teaser.findex
[01:04:21] [Teaser      ] csample /project/teaser/genometeaser/references/Gallus_gallus.fa 1100 0.010000
[01:04:22] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Gallus_gallus.fa.teaser.findex
[01:04:22] [Teaser      ] Sampling as contig: 9517 regions of size 1100 (pad 220), totalling 10469320 base pairs
[01:04:22] [Teaser      ] Sampling 9517 regions
[01:05:40] [Teaser      ] 10%
[01:06:10] [Teaser      ] 20%
[01:06:28] [Teaser      ] 30%
[01:06:39] [Teaser      ] 40%
[01:06:49] [Teaser      ] 50%
[01:06:58] [Teaser      ] 60%
[01:07:07] [Teaser      ] 70%
[01:07:16] [Teaser      ] 80%
[01:07:26] [Teaser      ] 90%
[01:07:35] [Teaser      ] 100%
[01:07:35] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a
[01:07:35] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 50000 --mp  --ll 100 --le 10  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Gallus_gallus.fa.sampled.100.1100.220.fasta
[01:07:35] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 50000 --mp  --ll 100 --le 10  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/Gallus_gallus.fa.sampled.100.1100.220.fasta
[01:09:15] [Teaser      ] move /project/teaser/genometeaser/references/Gallus_gallus.fa.sampled.100.1100.220.fasta_1.fastq -> ./reads1.fastq
[01:09:15] [Teaser      ] move /project/teaser/genometeaser/references/Gallus_gallus.fa.sampled.100.1100.220.fasta_2.fastq -> ./reads2.fastq
[01:09:15] [Teaser      ] move /project/teaser/genometeaser/references/Gallus_gallus.fa.sampled.100.1100.220.fasta.fastq.sam -> ./mapping_comparison.sam
[01:09:15] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a
[01:09:15] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[01:09:15] [Teaser      ] Translating SAM file coordinates (as contig)...
[01:09:15] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/Gallus_gallus.fa.teaser.findex
[01:09:33] [Teaser      ] remove /project/teaser/genometeaser/references/Gallus_gallus.fa.sampled.100.1100.220.fasta
[01:09:33] [Teaser      ] remove /project/teaser/genometeaser/references/Gallus_gallus.fa.sampled.100.1100.220.fasta.index
[01:09:33] [Teaser      ] remove mapping_comparison_unfixed.sam
[01:09:33] [Teaser      ] Took 312 seconds for generating 42fc1d552498df3b8ed5a53dd70b689a
[01:09:33] [Main        ] Data set creation completed
[01:09:33] [Main        ] 
[01:09:35] [bowtie2     ] 42fc1d552498df3b8ed5a53dd70b689a (base: tests_base/base_mapping)
[01:09:36] [init        ] Ref:   /project/teaser/genometeaser/references/Gallus_gallus.fa
[01:09:36] [init        ] Reads: /project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a/reads1.fastq
[01:09:36] [init        ] Output:/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a/out_bowtie2.sam
[01:09:36] [map         ] Command(pre): 
[01:09:36] [map         ] Base run time file not existing, performing base run
[01:09:36] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Gallus_gallus.fa_bt -U reads_base.fastq -S out_bowtie2.sam
[01:11:23] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie2/bowtie2  -p 4 -x /project/teaser/genometeaser/references/Gallus_gallus.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
[01:11:23] [map         ]    Mapping 32.00MB to 1065.00MB with bowtie2...
[01:11:41] [map         ]    Took 17.672 (wall), 50.320 (CPU) seconds, initialization time: 1.918 (wall), 1.904 (CPU) seconds.
[01:11:41] [map         ] Command(post): 
[01:11:41] [sort_prepare] Sorting...
[01:11:53] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[01:12:04] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
98248,1752,0,0,0,100000,0,0,0.98248,1.0,0.991162584238

[01:12:04] [bwa         ] 42fc1d552498df3b8ed5a53dd70b689a (base: tests_base/base_mapping)
[01:12:04] [init        ] Ref:   /project/teaser/genometeaser/references/Gallus_gallus.fa
[01:12:04] [init        ] Reads: /project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a/reads1.fastq
[01:12:04] [init        ] Output:/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a/out_bwa.sam
[01:12:04] [map         ] Command(pre): 
[01:12:04] [map         ] Base run time file not existing, performing base run
[01:12:04] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Gallus_gallus.fa reads_base.fastq  -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Gallus_gallus.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
[01:14:45] [map         ] Command(main): /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Gallus_gallus.fa reads1.fastq  -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Gallus_gallus.fa reads2.fastq  -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Gallus_gallus.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
[01:14:45] [map         ]    Mapping 32.00MB to 1065.00MB with bwa...
[01:15:23] [map         ]    Took 37.295 (wall), 69.072 (CPU) seconds, initialization time: 2.651 (wall), 2.480 (CPU) seconds.
[01:15:23] [map         ] Command(post): 
[01:15:23] [sort_prepare] Sorting...
[01:15:28] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[01:15:39] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
94526,1645,3829,0,0,100000,0,0,0.982895051523,0.961069594835,0.971859802803

[01:15:39] [bwamem      ] 42fc1d552498df3b8ed5a53dd70b689a (base: tests_base/base_mapping)
[01:15:39] [init        ] Ref:   /project/teaser/genometeaser/references/Gallus_gallus.fa
[01:15:39] [init        ] Reads: /project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a/reads1.fastq
[01:15:39] [init        ] Output:/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a/out_bwamem.sam
[01:15:39] [map         ] Command(pre): 
[01:15:39] [map         ] Base run time file not existing, performing base run
[01:15:39] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Gallus_gallus.fa reads_base.fastq  -t 4 > out_bwamem.sam
[01:15:43] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Gallus_gallus.fa reads1.fastq reads2.fastq  -t 4 > out_bwamem.sam
[01:15:43] [map         ]    Mapping 32.00MB to 1065.00MB with bwamem...
[01:15:55] [map         ]    Took 11.115 (wall), 24.380 (CPU) seconds, initialization time: 1.649 (wall), 1.544 (CPU) seconds.
[01:15:55] [map         ] Command(post): 
[01:15:56] [sort_prepare] Sorting...
[01:16:00] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[01:16:11] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
98448,1552,0,0,0,100000,0,0,0.98448,1.0,0.992179311457

[01:16:11] [bwasw       ] 42fc1d552498df3b8ed5a53dd70b689a (base: tests_base/base_mapping)
[01:16:11] [init        ] Ref:   /project/teaser/genometeaser/references/Gallus_gallus.fa
[01:16:11] [init        ] Reads: /project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a/reads1.fastq
[01:16:11] [init        ] Output:/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a/out_bwasw.sam
[01:16:11] [map         ] Command(pre): 
[01:16:11] [map         ] Base run time file not existing, performing base run
[01:16:11] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Gallus_gallus.fa reads_base.fastq  -t 4 > out_bwasw.sam
[01:16:15] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Gallus_gallus.fa reads1.fastq reads2.fastq  -t 4 > out_bwasw.sam
[01:16:15] [map         ]    Mapping 32.00MB to 1065.00MB with bwasw...
[01:17:10] [map         ]    Took 54.158 (wall), 117.560 (CPU) seconds, initialization time: 1.638 (wall), 1.540 (CPU) seconds.
[01:17:10] [map         ] Command(post): 
[01:17:10] [sort_prepare] Sorting...
[01:17:15] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[01:17:26] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
98250,1750,0,0,1,100000,0,0,0.9825,1.0,0.991172761665

[01:17:26] [ngm         ] 42fc1d552498df3b8ed5a53dd70b689a (base: tests_base/base_mapping)
[01:17:26] [init        ] Ref:   /project/teaser/genometeaser/references/Gallus_gallus.fa
[01:17:26] [init        ] Reads: /project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a/reads1.fastq
[01:17:26] [init        ] Output:/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a/out_ngm.sam
[01:17:26] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/Gallus_gallus.fa 
[01:20:38] [map         ] Base run time file not existing, performing base run
[01:20:38] [map         ] Command(pre-b): /project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/Gallus_gallus.fa -t 4 --qry reads_base.fastq  --no-progress
[01:20:52] [map         ] Command(main): /project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/Gallus_gallus.fa -t 4  --no-progress
[01:20:52] [map         ]    Mapping 32.00MB to 1065.00MB with ngm...
[01:21:08] [map         ]    Took 15.740 (wall), 30.684 (CPU) seconds, initialization time: 4.602 (wall), 4.708 (CPU) seconds.
[01:21:08] [map         ] Command(post): 
[01:21:08] [sort_prepare] Sorting...
[01:21:13] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[01:21:24] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
98378,1602,20,0,0,100000,0,0,0.983976795359,0.999796743836,0.991823690127