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
H_sapiensH_sapiens5500
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 Accession6a765d43cbdb960905eef4668388302e
Report timestampTue Oct 9 20:41:23 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/6a765d43cbdb960905eef4668388302e.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1539107832.454792
report: {name: 6a765d43cbdb960905eef4668388302e}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    6a765d43cbdb960905eef4668388302e: {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: 60,
      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: []
threads: 4
Log
[19:57:14] [Main        ] framework cmd:  ./teaser.py setups_generated/6a765d43cbdb960905eef4668388302e.yaml -mcpu
[19:57:14] [Main        ] framework hash: vevev
[19:57:14] [Main        ] deployment mode: devel (True)
[19:57:14] [Main        ] Test Runner Setup - ""

[19:57:14] [Main        ] Using Teaser for data set creation
[19:57:15] [Teaser      ] Init. Creating 1 test datasets.
[19:57:15] [Teaser      ] 
[19:57:15] [Teaser      ] Creating test 6a765d43cbdb960905eef4668388302e
[19:57:15] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e
[19:57:15] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e
[19:57:15] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[19:57:15] [Teaser      ] csample /project/teaser/genometeaser/references/H_sapiens.fa 1500 0.010000
[19:57:15] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[19:57:15] [Teaser      ] Sampling as contig: 20914 regions of size 1500 (pad 300), totalling 31371612 base pairs
[19:57:15] [Teaser      ] Sampling 20914 regions
[20:00:31] [Teaser      ] 10%
[20:02:04] [Teaser      ] 20%
[20:02:39] [Teaser      ] 30%
[20:02:54] [Teaser      ] 40%
[20:03:03] [Teaser      ] 50%
[20:03:09] [Teaser      ] 60%
[20:03:13] [Teaser      ] 70%
[20:03:16] [Teaser      ] 80%
[20:03:18] [Teaser      ] 90%
[20:03:21] [Teaser      ] 100%
[20:03:22] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e
[20:03:22] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 261430 --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
[20:03:22] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 261430 --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
[20:05:36] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta_1.fastq -> ./reads1.fastq
[20:05:36] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta_2.fastq -> ./reads2.fastq
[20:05:36] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta.fastq.sam -> ./mapping_comparison.sam
[20:05:36] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e
[20:05:36] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[20:05:36] [Teaser      ] Translating SAM file coordinates (as contig)...
[20:05:36] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[20:06:45] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta
[20:06:45] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.1500.300.fasta.index
[20:06:45] [Teaser      ] remove mapping_comparison_unfixed.sam
[20:06:45] [Teaser      ] Took 570 seconds for generating 6a765d43cbdb960905eef4668388302e
[20:06:45] [Main        ] Data set creation completed
[20:06:45] [Main        ] 
[20:06:47] [bowtie2     ] 6a765d43cbdb960905eef4668388302e (base: tests_base/base_mapping)
[20:06:47] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[20:06:47] [init        ] Reads: /project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e/reads1.fastq
[20:06:47] [init        ] Output:/project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e/out_bowtie2.sam
[20:06:48] [map         ] Command(pre): 
[20:06:48] [map         ] Base run time file not existing, performing base run
[20:06:48] [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
[20:11:42] [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
[20:11:42] [map         ]    Mapping 73.00MB to 3199.00MB with bowtie2...
[20:12:43] [map         ]    Took 60.911 (wall), 212.968 (CPU) seconds, initialization time: 3.787 (wall), 3.792 (CPU) seconds.
[20:12:43] [map         ] Command(post): 
[20:12:43] [sort_prepare] Sorting...
[20:13:18] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[20:14:06] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
501799,20605,456,0,0,522860,0,0,0.960557346422,0.999092094653,0.97944584491

[20:14:06] [bwa         ] 6a765d43cbdb960905eef4668388302e (base: tests_base/base_mapping)
[20:14:06] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[20:14:06] [init        ] Reads: /project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e/reads1.fastq
[20:14:06] [init        ] Output:/project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e/out_bwa.sam
[20:14:06] [map         ] Command(pre): 
[20:14:06] [map         ] Base run time file not existing, performing base run
[20:14:07] [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
[20:22:05] [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
[20:22:05] [map         ]    Mapping 73.00MB to 3199.00MB with bwa...
[20:24:29] [map         ]    Took 143.558 (wall), 254.664 (CPU) seconds, initialization time: 7.282 (wall), 7.156 (CPU) seconds.
[20:24:29] [map         ] Command(post): 
[20:24:29] [sort_prepare] Sorting...
[20:24:46] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[20:25:33] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
500202,20667,1991,0,0,522860,0,0,0.960322077144,0.996035388785,0.977852759657

[20:25:33] [bwamem      ] 6a765d43cbdb960905eef4668388302e (base: tests_base/base_mapping)
[20:25:33] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[20:25:33] [init        ] Reads: /project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e/reads1.fastq
[20:25:33] [init        ] Output:/project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e/out_bwamem.sam
[20:25:33] [map         ] Command(pre): 
[20:25:33] [map         ] Base run time file not existing, performing base run
[20:25:33] [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
[20:25:43] [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
[20:25:43] [map         ]    Mapping 73.00MB to 3199.00MB with bwamem...
[20:26:56] [map         ]    Took 72.333 (wall), 228.228 (CPU) seconds, initialization time: 4.458 (wall), 4.384 (CPU) seconds.
[20:26:56] [map         ] Command(post): 
[20:26:56] [sort_prepare] Sorting...
[20:27:11] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[20:27:57] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
503968,18892,0,0,0,522860,0,0,0.963867957006,1.0,0.981601592477

[20:27:57] [bwasw       ] 6a765d43cbdb960905eef4668388302e (base: tests_base/base_mapping)
[20:27:57] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[20:27:57] [init        ] Reads: /project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e/reads1.fastq
[20:27:57] [init        ] Output:/project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e/out_bwasw.sam
[20:27:57] [map         ] Command(pre): 
[20:27:57] [map         ] Base run time file not existing, performing base run
[20:27:57] [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
[20:28:08] [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
[20:28:08] [map         ]    Mapping 73.00MB to 3199.00MB with bwasw...
[20:30:08] [map         ]    Took 120.068 (wall), 263.964 (CPU) seconds, initialization time: 4.480 (wall), 4.400 (CPU) seconds.
[20:30:08] [map         ] Command(post): 
[20:30:08] [sort_prepare] Sorting...
[20:30:22] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[20:31:08] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
494035,27188,1636,1,44,522860,1,0,0.947838065473,0.99669942361,0.971654862749

[20:31:08] [ngm         ] 6a765d43cbdb960905eef4668388302e (base: tests_base/base_mapping)
[20:31:08] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[20:31:08] [init        ] Reads: /project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e/reads1.fastq
[20:31:08] [init        ] Output:/project/teaser/genometeaser/tests_generated/6a765d43cbdb960905eef4668388302e/out_ngm.sam
[20:31:08] [map         ] Command(pre): 
[20:31:08] [map         ] Base run time file not existing, performing base run
[20:31:09] [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
[20:39:35] [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
[20:39:35] [map         ]    Mapping 73.00MB to 3199.00MB with ngm...
[20:40:21] [map         ]    Took 45.853 (wall), 125.036 (CPU) seconds, initialization time: 8.468 (wall), 8.640 (CPU) seconds.
[20:40:21] [map         ] Command(post): 
[20:40:21] [sort_prepare] Sorting...
[20:40:37] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 30)... 
[20:41:23] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
487428,29188,6242,2,0,522860,0,0,0.943501556282,0.987355926023,0.964930722587