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, 1 fail, 0 aborted, 0 errors total.
StateNameReferenceExecutedOKWarningsErrors
M_musculusM_musculus5401
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 Accession3f55d5f326042c6d121b7048b0ae8ccd
Report timestampFri Jul 13 17:49:04 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/3f55d5f326042c6d121b7048b0ae8ccd.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 11}
include: [base_teaser.yaml]
meta_timestamp: 1531175138.186108
report: {name: 3f55d5f326042c6d121b7048b0ae8ccd}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    3f55d5f326042c6d121b7048b0ae8ccd: {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: 22, 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
[16:26:47] [Main        ] framework cmd:  ./teaser.py setups_generated/3f55d5f326042c6d121b7048b0ae8ccd.yaml -mcpu
[16:26:47] [Main        ] framework hash: vevev
[16:26:47] [Main        ] deployment mode: devel (True)
[16:26:47] [Main        ] Test Runner Setup - ""

[16:26:47] [Main        ] Using Teaser for data set creation
[16:26:47] [Teaser      ] Init. Creating 1 test datasets.
[16:26:47] [Teaser      ] 
[16:26:47] [Teaser      ] Creating test 3f55d5f326042c6d121b7048b0ae8ccd
[16:26:47] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd
[16:26:47] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd
[16:26:47] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus.fasta.teaser.findex
[16:26:47] [Teaser      ] csample /project/teaser/genometeaser/references/M_musculus.fasta 220 0.010000
[16:26:47] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus.fasta.teaser.findex
[16:26:47] [Teaser      ] Sampling as contig: 219928 regions of size 220 (pad 44), totalling 48384255 base pairs
[16:26:47] [Teaser      ] Sampling 219928 regions
[16:35:22] [Teaser      ] 10%
[16:36:05] [Teaser      ] 20%
[16:36:48] [Teaser      ] 30%
[16:37:33] [Teaser      ] 40%
[16:38:18] [Teaser      ] 50%
[16:39:01] [Teaser      ] 60%
[16:39:46] [Teaser      ] 70%
[16:40:33] [Teaser      ] 80%
[16:41:17] [Teaser      ] 90%
[16:42:05] [Teaser      ] 100%
[16:42:12] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd
[16:42:12] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 22 -N 2199284  --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.100.220.44.fasta
[16:42:12] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 22 -N 2199284  --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.100.220.44.fasta
[16:45:46] [Teaser      ] move /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.220.44.fasta.fastq -> ./reads.fastq
[16:45:46] [Teaser      ] move /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.220.44.fasta.fastq.sam -> ./mapping_comparison.sam
[16:45:46] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd
[16:45:46] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[16:45:46] [Teaser      ] Translating SAM file coordinates (as contig)...
[16:45:46] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/M_musculus.fasta.teaser.findex
[16:51:43] [Teaser      ] remove /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.220.44.fasta
[16:51:43] [Teaser      ] remove /project/teaser/genometeaser/references/M_musculus.fasta.sampled.100.220.44.fasta.index
[16:51:43] [Teaser      ] remove mapping_comparison_unfixed.sam
[16:51:43] [Teaser      ] Took 1496 seconds for generating 3f55d5f326042c6d121b7048b0ae8ccd
[16:51:43] [Main        ] Data set creation completed
[16:51:43] [Main        ] 
[16:51:44] [bowtie2     ] 3f55d5f326042c6d121b7048b0ae8ccd (base: tests_base/base_mapping)
[16:51:44] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[16:51:44] [init        ] Reads: /project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd/reads.fastq
[16:51:44] [init        ] Output:/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd/out_bowtie2.sam
[16:51:44] [map         ] Command(pre): 
[16:51:44] [map         ] Base run time file not existing, performing base run
[16:51:44] [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
[16:56:14] [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
[16:56:14] [map         ]    Mapping 140.00MB to 4919.00MB with bowtie2...
[16:57:53] [map         ]    Took 97.349 (wall), 349.332 (CPU) seconds, initialization time: 3.460 (wall), 3.492 (CPU) seconds.
[16:57:53] [map         ] Command(post): 
[16:57:53] [sort_prepare] Sorting...
[17:00:41] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 11)... 
[17:03:34] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
1611227,508730,79327,0,0,2199284,5,0,0.760028151514,0.953076328825,0.845675028887

[17:03:34] [bwa         ] 3f55d5f326042c6d121b7048b0ae8ccd (base: tests_base/base_mapping)
[17:03:34] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[17:03:34] [init        ] Reads: /project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd/reads.fastq
[17:03:34] [init        ] Output:/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd/out_bwa.sam
[17:03:34] [map         ] Command(pre): 
[17:03:34] [map         ] Base run time file not existing, performing base run
[17:03:34] [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
[17:15:54] [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
[17:15:54] [map         ]    Mapping 140.00MB to 4919.00MB with bwa...
[17:21:11] [map         ]    Took 316.880 (wall), 746.464 (CPU) seconds, initialization time: 12.844 (wall), 12.680 (CPU) seconds.
[17:21:11] [map         ] Command(post): 
[17:21:11] [sort_prepare] Sorting...
[17:22:19] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 11)... 
[17:25:11] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
1634861,562351,2072,0,0,2199284,6,0,0.744061565293,0.9987342182,0.852790387427

[17:25:11] [bwamem      ] 3f55d5f326042c6d121b7048b0ae8ccd (base: tests_base/base_mapping)
[17:25:11] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[17:25:11] [init        ] Reads: /project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd/reads.fastq
[17:25:11] [init        ] Output:/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd/out_bwamem.sam
[17:25:11] [map         ] Command(pre): 
[17:25:11] [map         ] Base run time file not existing, performing base run
[17:25:11] [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
[17:25:28] [map         ] Command(main): /project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq  -t 4 > out_bwamem.sam
[17:25:28] [map         ]    Mapping 140.00MB to 4919.00MB with bwamem...
[17:28:27] [map         ]    Took 178.947 (wall), 658.372 (CPU) seconds, initialization time: 7.811 (wall), 7.708 (CPU) seconds.
[17:28:27] [map         ] Command(post): 
[17:28:27] [sort_prepare] Sorting...
[17:28:27] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 11)... 
[17:30:01] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
0,0,0,2199284,0,2199284,0,0,0,0,0
[17:30:01] [calc_stats  ] Unexpectedly reached end of mapper output at sorted_out_bwamem.sam:read.000000000
[17:30:01] [calc_stats  ] None

[17:30:01] [bwamem      ] Errors in test, not caching!

[17:30:01] [bwasw       ] 3f55d5f326042c6d121b7048b0ae8ccd (base: tests_base/base_mapping)
[17:30:01] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[17:30:01] [init        ] Reads: /project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd/reads.fastq
[17:30:01] [init        ] Output:/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd/out_bwasw.sam
[17:30:01] [map         ] Command(pre): 
[17:30:01] [map         ] Base run time file not existing, performing base run
[17:30:01] [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
[17:30:17] [map         ] Command(main): /project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq  -t 4 > out_bwasw.sam
[17:30:17] [map         ]    Mapping 140.00MB to 4919.00MB with bwasw...
[17:30:50] [map         ]    Took 31.724 (wall), 26.232 (CPU) seconds, initialization time: 7.861 (wall), 7.776 (CPU) seconds.
[17:30:50] [map         ] Command(post): 
[17:30:50] [sort_prepare] Sorting...
[17:31:39] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 11)... 
[17:33:49] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
0,0,2199284,0,0,2199284,0,0,0,0,0

[17:33:49] [ngm         ] 3f55d5f326042c6d121b7048b0ae8ccd (base: tests_base/base_mapping)
[17:33:49] [init        ] Ref:   /project/teaser/genometeaser/references/M_musculus.fasta
[17:33:49] [init        ] Reads: /project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd/reads.fastq
[17:33:49] [init        ] Output:/project/teaser/genometeaser/tests_generated/3f55d5f326042c6d121b7048b0ae8ccd/out_ngm.sam
[17:33:49] [map         ] Command(pre): /project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/M_musculus.fasta 
[17:43:15] [map         ] Base run time file not existing, performing base run
[17:43:15] [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
[17:43:36] [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
[17:43:36] [map         ]    Mapping 140.00MB to 4919.00MB with ngm...
[17:45:05] [map         ]    Took 88.947 (wall), 276.424 (CPU) seconds, initialization time: 9.599 (wall), 9.776 (CPU) seconds.
[17:45:05] [map         ] Command(post): 
[17:45:05] [sort_prepare] Sorting...
[17:46:13] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 11)... 
[17:49:04] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
1572741,485470,141073,0,0,2199284,12,0,0.764130111053,0.917684766258,0.833897442355