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, 2 fail, 0 aborted, 0 errors total.
StateNameReferenceExecutedOKWarningsErrors
H_sapiensH_sapiens5302
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 Accessioncc90747119948fac5bcca0e53c33f3a3
Report timestampThu May 11 03:55:29 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/cc90747119948fac5bcca0e53c33f3a3.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 50}
include: [base_teaser.yaml]
meta_timestamp: 1494466559.708138
report: {name: cc90747119948fac5bcca0e53c33f3a3}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    cc90747119948fac5bcca0e53c33f3a3: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 175,
      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: 100,
      reference: !!python/unicode 'H_sapiens.fa', simulator: !!python/unicode 'dwgsim',
      title: !!python/unicode 'H_sapiens', type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, ngm, segemehl]
test_parameters: []
threads: 4
Log
[03:36:01] [Main        ] framework cmd:  ./teaser.py setups_generated/cc90747119948fac5bcca0e53c33f3a3.yaml -mcpu
[03:36:01] [Main        ] framework hash: vevev
[03:36:01] [Main        ] deployment mode: devel (True)
[03:36:01] [Main        ] Test Runner Setup - ""

[03:36:01] [Main        ] Using Teaser for data set creation
[03:36:01] [Teaser      ] Init. Creating 1 test datasets.
[03:36:01] [Teaser      ] 
[03:36:01] [Teaser      ] Creating test cc90747119948fac5bcca0e53c33f3a3
[03:36:01] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3
[03:36:01] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3
[03:36:01] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[03:36:01] [Teaser      ] csample /project/teaser/genometeaser/references/H_sapiens.fa 2250 0.010000
[03:36:01] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[03:36:01] [Teaser      ] Sampling as contig: 13942 regions of size 2250 (pad 450), totalling 31371612 base pairs
[03:36:01] [Teaser      ] Sampling 13942 regions
[03:36:31] [Teaser      ] 10%
[03:36:36] [Teaser      ] 20%
[03:36:37] [Teaser      ] 30%
[03:36:37] [Teaser      ] 40%
[03:36:38] [Teaser      ] 50%
[03:36:39] [Teaser      ] 60%
[03:36:39] [Teaser      ] 70%
[03:36:40] [Teaser      ] 80%
[03:36:40] [Teaser      ] 90%
[03:36:41] [Teaser      ] 100%
[03:36:41] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3
[03:36:41] [Teaser      ] subprogram /project/teaser/genometeaser/software/dwgsim -c 0 -1 100 -2 100 -N 156858 -d 175 -s 50  -r 0.001000  -R 0.300000  -y 0  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.2250.450.fasta dwgout
[03:37:03] [Teaser      ] move enc_dwgout.bwa.read1.fastq -> reads1.fastq
[03:37:03] [Teaser      ] move enc_dwgout.bwa.read2.fastq -> reads2.fastq
[03:37:03] [Teaser      ] move enc_dwgout.bwa.read1.fastq.sam -> mapping_comparison.sam
[03:37:03] [Teaser      ] remove dwgout.bwa.read1.fastq.sam
[03:37:03] [Teaser      ] remove dwgout.mutations.txt
[03:37:03] [Teaser      ] remove dwgout.mutations.vcf
[03:37:03] [Teaser      ] remove dwgout.bfast.fastq
[03:37:03] [Teaser      ] remove dwgout.bwa.read1.fastq
[03:37:03] [Teaser      ] remove dwgout.bwa.read2.fastq
[03:37:03] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3
[03:37:03] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[03:37:03] [Teaser      ] Translating SAM file coordinates (as contig)...
[03:37:03] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[03:37:11] [Teaser      ] Warning: Len of source sample set = 0, read Y29udGlnXzMzMjUwNDkxXzMzMjUwNTIxXzBfMV8wXzBfMTowOjBfMzowOjBfMTM0Yzc=
[03:37:13] [Teaser      ] Warning: Len of source sample set = 0, read Y29udGlnXzMzMjUwNDA3XzMzMjUwMzMxXzFfMF8wXzBfMTowOjBfMDowOjBfMTkzOTA=
[03:37:13] [Teaser      ] Warning: Len of source sample set = 0, read Y29udGlnXzMzMjUwNDA3XzMzMjUwMzMxXzFfMF8wXzBfMTowOjBfMDowOjBfMTkzOTA=
[03:37:19] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.2250.450.fasta
[03:37:19] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.2250.450.fasta.index
[03:37:19] [Teaser      ] remove mapping_comparison_unfixed.sam
[03:37:19] [Teaser      ] Took 78 seconds for generating cc90747119948fac5bcca0e53c33f3a3
[03:37:19] [Main        ] Data set creation completed
[03:37:19] [Main        ] 
[03:37:20] [bowtie2     ] cc90747119948fac5bcca0e53c33f3a3 (base: tests_base/base_mapping)
[03:37:20] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[03:37:20] [init        ] Reads: /project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3/reads1.fastq
[03:37:20] [init        ] Output:/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3/out_bowtie2.sam
[03:37:20] [map         ] Command(pre): 
[03:37:20] [map         ] Base run time file not existing, performing base run
[03:37:20] [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
[03:37:58] [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
[03:37:58] [map         ]    Mapping 86.00MB to 3199.00MB with bowtie2...
[03:38:45] [map         ]    Took 46.056 (wall), 175.450 (CPU) seconds, initialization time: 7.817 (wall), 2.328 (CPU) seconds.
[03:38:45] [map         ] Command(post): 
[03:38:45] [sort_prepare] Sorting...
[03:38:54] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[03:39:03] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
300577,11176,1960,0,3,313713,0,0,0.964151106806,0.993521453574,0.978615963144

[03:39:03] [bwa         ] cc90747119948fac5bcca0e53c33f3a3 (base: tests_base/base_mapping)
[03:39:03] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[03:39:03] [init        ] Reads: /project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3/reads1.fastq
[03:39:03] [init        ] Output:/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3/out_bwa.sam
[03:39:03] [map         ] Command(pre): 
[03:39:03] [map         ] Base run time file not existing, performing base run
[03:39:03] [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
[03:40:01] [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
[03:40:01] [map         ]    Mapping 86.00MB to 3199.00MB with bwa...
[03:42:34] [map         ]    Took 152.766 (wall), 328.085 (CPU) seconds, initialization time: 6.783 (wall), 4.584 (CPU) seconds.
[03:42:34] [map         ] Command(post): 
[03:42:34] [sort_prepare] Sorting...
[03:42:39] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[03:42:47] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
302379,8900,2434,0,3,313713,0,0,0.971408286457,0.992014776273,0.981603396895

[03:42:47] [bwamem      ] cc90747119948fac5bcca0e53c33f3a3 (base: tests_base/base_mapping)
[03:42:48] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[03:42:48] [init        ] Reads: /project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3/reads1.fastq
[03:42:48] [init        ] Output:/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3/out_bwamem.sam
[03:42:48] [map         ] Command(pre): 
[03:42:48] [map         ] Base run time file not existing, performing base run
[03:42:48] [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
[03:42:54] [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
[03:42:54] [map         ]    Mapping 86.00MB to 3199.00MB with bwamem...
[03:43:39] [map         ]    Took 44.368 (wall), 161.859 (CPU) seconds, initialization time: 2.922 (wall), 2.878 (CPU) seconds.
[03:43:39] [map         ] Command(post): 
[03:43:39] [sort_prepare] Sorting...
[03:43:43] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[03:43:51] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
305487,8226,0,0,3,313713,0,3,0.97377858106,1.0,0.986715116279

[03:43:51] [ngm         ] cc90747119948fac5bcca0e53c33f3a3 (base: tests_base/base_mapping)
[03:43:51] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[03:43:51] [init        ] Reads: /project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3/reads1.fastq
[03:43:51] [init        ] Output:/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3/out_ngm.sam
[03:43:51] [map         ] Command(pre): 
[03:43:51] [map         ] Base run time file not existing, performing base run
[03:43:51] [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
[03:45:33] [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
[03:45:33] [map         ]    Mapping 86.00MB to 3199.00MB with ngm...
[03:46:01] [map         ]    Took 27.064 (wall), 6.967 (CPU) seconds, initialization time: 49.236 (wall), 6.501 (CPU) seconds.
[03:46:01] [map         ] Command(post): 
[03:46:01] [sort_prepare] Sorting...
[03:46:01] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[03:46:05] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
0,0,0,313713,0,313713,0,0,0,0,0
[03:46:05] [calc_stats  ] Unexpectedly reached end of mapper output at sorted_out_ngm.sam:Y29udGlnXzc0MDA4OTJfNzQwMDk3Ml8wXzFfMF8wXzI6MDowXzA6MDowXzczMmQ=
[03:46:05] [calc_stats  ] None

[03:46:05] [ngm         ] Errors in test, not caching!

[03:46:05] [segemehl    ] cc90747119948fac5bcca0e53c33f3a3 (base: tests_base/base_mapping)
[03:46:05] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[03:46:05] [init        ] Reads: /project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3/reads1.fastq
[03:46:05] [init        ] Output:/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3/out_segemehl.sam
[03:46:05] [map         ] Command(pre): /project/teaser/genometeaser/software/segemehl.x -x /project/teaser/genometeaser/references/H_sapiens.fa.idx -d /project/teaser/genometeaser/references/H_sapiens.fa
[03:52:09] [map         ] Base run time file not existing, performing base run
[03:52:09] [map         ] Command(pre-b): /project/teaser/genometeaser/software/segemehl.x  -r 1 -i /project/teaser/genometeaser/references/H_sapiens.fa.idx -d /project/teaser/genometeaser/references/H_sapiens.fa -q reads_base.fastq > out_segemehl.sam
[03:54:20] [map         ] Command(main): /project/teaser/genometeaser/software/segemehl.x  -r 1 -i /project/teaser/genometeaser/references/H_sapiens.fa.idx -d /project/teaser/genometeaser/references/H_sapiens.fa -q reads1.fastq -p reads2.fastq > out_segemehl.sam
[03:54:20] [map         ]    Mapping 86.00MB to 3199.00MB with segemehl...
[03:55:24] [map         ]    Took 63.517 (wall), 63.269 (CPU) seconds, initialization time: 62.331 (wall), 62.135 (CPU) seconds.
[03:55:24] [map         ] Command(post): 
[03:55:24] [sort_prepare] Sorting...
[03:55:24] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... 
[03:55:29] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
0,0,0,313713,0,313713,0,0,0,0,0
[03:55:29] [calc_stats  ] Unexpectedly reached end of mapper output at sorted_out_segemehl.sam:Y29udGlnXzc0MDA4OTJfNzQwMDk3Ml8wXzFfMF8wXzI6MDowXzA6MDowXzczMmQ=
[03:55:29] [calc_stats  ] None

[03:55:29] [segemehl    ] Errors in test, not caching!