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.

10 tests executed, 1 fail, 0 aborted, 0 errors total.
StateNameReferenceExecutedOKWarningsErrors
H_sapiensH_sapiens10901
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 Accession9981dd417977dbaa7d58a80ddba44b12
Report timestampFri Jul 13 18:45:35 2018
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser
Framework Command Line./teaser.py setups_generated/9981dd417977dbaa7d58a80ddba44b12.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 75}
include: [base_teaser.yaml]
meta_timestamp: 1531309661.544162
report: {name: 9981dd417977dbaa7d58a80ddba44b12}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    9981dd417977dbaa7d58a80ddba44b12: {coverage: 1.0, error_rate_mult: 1.0, insert_size: 250,
      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: 150,
      reference: !!python/unicode 'H_sapiens.fa', title: !!python/unicode 'H_sapiens',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie, bowtie2, bwa, bwamem, bwasw, cushaw3, ngm, ngm_0_4_11, segemehl,
  stampy]
test_parameters: []
threads: 4
Log
[17:49:08] [Main        ] framework cmd:  ./teaser.py setups_generated/9981dd417977dbaa7d58a80ddba44b12.yaml -mcpu
[17:49:08] [Main        ] framework hash: vevev
[17:49:08] [Main        ] deployment mode: devel (True)
[17:49:08] [Main        ] Test Runner Setup - ""

[17:49:08] [Main        ] Using Teaser for data set creation
[17:49:08] [Teaser      ] Init. Creating 1 test datasets.
[17:49:08] [Teaser      ] 
[17:49:08] [Teaser      ] Creating test 9981dd417977dbaa7d58a80ddba44b12
[17:49:08] [Teaser      ] Failed to create test directory, probably existing
[17:49:08] [Teaser      ] remove /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/9981dd417977dbaa7d58a80ddba44b12.yaml
[17:49:08] [Teaser      ] remove /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/mapping_comparison.sam
[17:49:08] [Teaser      ] remove /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads.fastq
[17:49:08] [Teaser      ] remove /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads1.fastq
[17:49:08] [Teaser      ] remove /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads2.fastq
[17:49:08] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12
[17:49:08] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12
[17:49:08] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[17:49:08] [Teaser      ] csample /project/teaser/genometeaser/references/H_sapiens.fa 3000 0.010000
[17:49:08] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[17:49:08] [Teaser      ] Sampling as contig: 10457 regions of size 3000 (pad 600), totalling 31371612 base pairs
[17:49:08] [Teaser      ] Sampling 10457 regions
[17:49:09] [Teaser      ] 10%
[17:49:10] [Teaser      ] 20%
[17:49:12] [Teaser      ] 30%
[17:49:13] [Teaser      ] 40%
[17:49:14] [Teaser      ] 50%
[17:49:15] [Teaser      ] 60%
[17:49:16] [Teaser      ] 70%
[17:49:18] [Teaser      ] 80%
[17:49:19] [Teaser      ] 90%
[17:49:20] [Teaser      ] 100%
[17:49:24] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12
[17:49:24] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 104572 --mp  --ll 250 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.3000.600.fasta
[17:49:24] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 150 -N 104572 --mp  --ll 250 --le 50  --hi 0.000300  --hs 0.000700  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.3000.600.fasta
[17:52:50] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.3000.600.fasta_1.fastq -> ./reads1.fastq
[17:52:50] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.3000.600.fasta_2.fastq -> ./reads2.fastq
[17:52:50] [Teaser      ] move /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.3000.600.fasta.fastq.sam -> ./mapping_comparison.sam
[17:52:50] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12
[17:52:50] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[17:52:50] [Teaser      ] Translating SAM file coordinates (as contig)...
[17:52:50] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/H_sapiens.fa.teaser.findex
[17:53:24] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.3000.600.fasta
[17:53:24] [Teaser      ] remove /project/teaser/genometeaser/references/H_sapiens.fa.sampled.100.3000.600.fasta.index
[17:53:24] [Teaser      ] remove mapping_comparison_unfixed.sam
[17:53:24] [Teaser      ] Took 256 seconds for generating 9981dd417977dbaa7d58a80ddba44b12
[17:53:25] [Main        ] Data set creation completed
[17:53:25] [Main        ] 
[17:53:25] [bowtie      ] 9981dd417977dbaa7d58a80ddba44b12 (base: tests_base/base_mapping)
[17:53:25] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[17:53:25] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads1.fastq
[17:53:25] [init        ] Output:/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/out_bowtie.sam
[17:53:25] [map         ] Command(pre): 
[17:53:25] [map         ] Base run time file not existing, performing base run
[17:53:26] [map         ] Command(pre-b): /project/teaser/genometeaser/software/bowtie --threads 4  -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads_base.fastq out_bowtie.sam
[17:56:53] [map         ] Command(main): /project/teaser/genometeaser/software/bowtie --threads 4  -S /project/teaser/genometeaser/references/H_sapiens.fa_bo -1 reads1.fastq -2 reads2.fastq out_bowtie.sam
[17:56:53] [map         ]    Mapping 66.00MB to 3199.00MB with bowtie...
[17:58:36] [map         ]    Took 102.508 (wall), 151.608 (CPU) seconds, initialization time: 2.729 (wall), 2.648 (CPU) seconds.
[17:58:36] [map         ] Command(post): 
[17:58:36] [sort_prepare] Sorting...
[17:59:00] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[17:59:19] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
51267,1403,156474,0,0,209144,0,0,0.973362445415,0.246783254148,0.393739127763

[17:59:19] [bowtie2     ] 9981dd417977dbaa7d58a80ddba44b12 (base: tests_base/base_mapping)
[17:59:19] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[17:59:19] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads1.fastq
[17:59:19] [init        ] Output:/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/out_bowtie2.sam
[17:59:19] [map         ] Command(pre): 
[17:59:19] [map         ] Base run time file not existing, performing base run
[17:59:19] [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
[17:59:27] [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
[17:59:27] [map         ]    Mapping 66.00MB to 3199.00MB with bowtie2...
[18:00:12] [map         ]    Took 44.470 (wall), 151.040 (CPU) seconds, initialization time: 3.496 (wall), 3.508 (CPU) seconds.
[18:00:12] [map         ] Command(post): 
[18:00:13] [sort_prepare] Sorting...
[18:00:25] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[18:00:47] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
204775,4319,50,0,0,209144,0,0,0.97934421839,0.999755889174,0.989444794755

[18:00:47] [bwa         ] 9981dd417977dbaa7d58a80ddba44b12 (base: tests_base/base_mapping)
[18:00:47] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:00:47] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads1.fastq
[18:00:47] [init        ] Output:/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/out_bwa.sam
[18:00:47] [map         ] Command(pre): 
[18:00:47] [map         ] Base run time file not existing, performing base run
[18:00:47] [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
[18:01:03] [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
[18:01:03] [map         ]    Mapping 66.00MB to 3199.00MB with bwa...
[18:03:23] [map         ]    Took 139.221 (wall), 301.840 (CPU) seconds, initialization time: 7.390 (wall), 7.192 (CPU) seconds.
[18:03:23] [map         ] Command(post): 
[18:03:23] [sort_prepare] Sorting...
[18:03:35] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[18:03:57] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
203440,4928,776,0,0,209144,0,0,0.976349535437,0.996200101853,0.986174936498

[18:03:58] [bwamem      ] 9981dd417977dbaa7d58a80ddba44b12 (base: tests_base/base_mapping)
[18:03:58] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:03:58] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads1.fastq
[18:03:58] [init        ] Output:/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/out_bwamem.sam
[18:03:58] [map         ] Command(pre): 
[18:03:58] [map         ] Base run time file not existing, performing base run
[18:03:58] [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
[18:04:08] [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
[18:04:08] [map         ]    Mapping 66.00MB to 3199.00MB with bwamem...
[18:04:47] [map         ]    Took 38.161 (wall), 107.776 (CPU) seconds, initialization time: 4.694 (wall), 4.632 (CPU) seconds.
[18:04:47] [map         ] Command(post): 
[18:04:47] [sort_prepare] Sorting...
[18:04:59] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[18:05:21] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
204958,4186,0,0,0,209144,0,0,0.979985082049,1.0,0.989891379419

[18:05:21] [bwasw       ] 9981dd417977dbaa7d58a80ddba44b12 (base: tests_base/base_mapping)
[18:05:21] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:05:21] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads1.fastq
[18:05:21] [init        ] Output:/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/out_bwasw.sam
[18:05:21] [map         ] Command(pre): 
[18:05:21] [map         ] Base run time file not existing, performing base run
[18:05:21] [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
[18:05:31] [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
[18:05:31] [map         ]    Mapping 66.00MB to 3199.00MB with bwasw...
[18:08:37] [map         ]    Took 185.863 (wall), 458.040 (CPU) seconds, initialization time: 4.682 (wall), 4.612 (CPU) seconds.
[18:08:37] [map         ] Command(post): 
[18:08:37] [sort_prepare] Sorting...
[18:08:49] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[18:09:11] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
203933,5211,0,0,8,209144,0,0,0.975084152546,1.0,0.98738491855

[18:09:11] [cushaw3     ] 9981dd417977dbaa7d58a80ddba44b12 (base: tests_base/base_mapping)
[18:09:11] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:09:11] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads1.fastq
[18:09:11] [init        ] Output:/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/out_cushaw3.sam
[18:09:11] [map         ] Command(pre): 
[18:09:11] [map         ] Base run time file not existing, performing base run
[18:09:11] [map         ] Command(pre-b): /project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/H_sapiens.fa_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1
[18:14:17] [map         ] Command(main): /project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/H_sapiens.fa_cushaw3 -q reads1.fastq reads2.fastq -o out_cushaw3.sam -t 4 -multi 1
[18:14:17] [map         ]    Mapping 66.00MB to 3199.00MB with cushaw3...
[18:16:01] [map         ]    Took 103.181 (wall), 394.832 (CPU) seconds, initialization time: 3.824 (wall), 3.680 (CPU) seconds.
[18:16:01] [map         ] Command(post): 
[18:16:01] [sort_prepare] Sorting...
[18:16:12] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[18:16:31] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
204733,4411,0,0,0,209144,0,0,0.978909268255,1.0,0.989342244193

[18:16:31] [ngm         ] 9981dd417977dbaa7d58a80ddba44b12 (base: tests_base/base_mapping)
[18:16:31] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:16:31] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads1.fastq
[18:16:31] [init        ] Output:/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/out_ngm.sam
[18:16:31] [map         ] Command(pre): 
[18:16:31] [map         ] Base run time file not existing, performing base run
[18:16:31] [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
[18:16:47] [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
[18:16:47] [map         ]    Mapping 66.00MB to 3199.00MB with ngm...
[18:17:33] [map         ]    Took 45.384 (wall), 108.824 (CPU) seconds, initialization time: 7.617 (wall), 7.788 (CPU) seconds.
[18:17:33] [map         ] Command(post): 
[18:17:34] [sort_prepare] Sorting...
[18:17:45] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[18:18:08] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
203519,5461,164,0,0,209144,0,0,0.973868312757,0.999194827256,0.986369022665

[18:18:08] [ngm_0_4_11  ] 9981dd417977dbaa7d58a80ddba44b12 (base: tests_base/base_mapping)
[18:18:08] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:18:08] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads1.fastq
[18:18:08] [init        ] Output:/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/out_ngm_0_4_11.sam
[18:18:08] [map         ] Command(pre): 
[18:18:08] [map         ] Base run time file not existing, performing base run
[18:18:08] [map         ] Command(pre-b): /software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq  --no-progress
[18:18:24] [map         ] Command(main): /software/ngm/bin-linux/ngm-0.4.11 --qry2 reads2.fastq --output out_ngm_0_4_11.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4  --no-progress
[18:18:24] [map         ]    Mapping 66.00MB to 3199.00MB with ngm_0_4_11...
[18:19:08] [map         ]    Took 43.082 (wall), 109.536 (CPU) seconds, initialization time: 7.110 (wall), 7.344 (CPU) seconds.
[18:19:08] [map         ] Command(post): 
[18:19:08] [sort_prepare] Sorting...
[18:19:20] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[18:19:42] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
203518,5486,140,0,0,209144,0,0,0.973751698532,0.999312573039,0.986366566342

[18:19:42] [segemehl    ] 9981dd417977dbaa7d58a80ddba44b12 (base: tests_base/base_mapping)
[18:19:42] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:19:42] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads1.fastq
[18:19:42] [init        ] Output:/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/out_segemehl.sam
[18:19:42] [map         ] Command(pre): 
[18:19:42] [map         ] Base run time file not existing, performing base run
[18:19:42] [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
[18:27:26] [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
[18:27:26] [map         ]    Mapping 66.00MB to 3199.00MB with segemehl...
[18:30:23] [map         ]    Took 177.068 (wall), 176.964 (CPU) seconds, initialization time: 173.259 (wall), 173.200 (CPU) seconds.
[18:30:23] [map         ] Command(post): 
[18:30:23] [sort_prepare] Sorting...
[18:30:23] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[18:30:35] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
0,0,0,209144,0,209144,0,0,0,0,0
[18:30:35] [calc_stats  ] Unexpectedly reached end of mapper output at sorted_out_segemehl.sam:read.000000000
[18:30:35] [calc_stats  ] None

[18:30:35] [segemehl    ] Errors in test, not caching!

[18:30:35] [stampy      ] 9981dd417977dbaa7d58a80ddba44b12 (base: tests_base/base_mapping)
[18:30:35] [init        ] Ref:   /project/teaser/genometeaser/references/H_sapiens.fa
[18:30:35] [init        ] Reads: /project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/reads1.fastq
[18:30:35] [init        ] Output:/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12/out_stampy.sam
[18:30:35] [map         ] Command(pre): 
[18:30:35] [map         ] Base run time file not existing, performing base run
[18:30:35] [map         ] Command(pre-b): /project/teaser/genometeaser/software/stampy  -t 4 -g /project/teaser/genometeaser/references/H_sapiens.fa_o -h /project/teaser/genometeaser/references/H_sapiens.fa_o -M reads_base.fastq -o out_stampy.sam
[18:30:40] [map         ] Command(main): /project/teaser/genometeaser/software/stampy  -t 4 -g /project/teaser/genometeaser/references/H_sapiens.fa_o -h /project/teaser/genometeaser/references/H_sapiens.fa_o -o out_stampy.sam -M reads1.fastq reads2.fastq
[18:30:40] [map         ]    Mapping 66.00MB to 3199.00MB with stampy...
[18:45:01] [map         ]    Took 860.640 (wall), 3512.056 (CPU) seconds, initialization time: 1.346 (wall), 1.180 (CPU) seconds.
[18:45:01] [map         ] Command(post): 
[18:45:01] [sort_prepare] Sorting...
[18:45:13] [calc_stats  ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 75)... 
[18:45:35] [calc_stats  ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure
204377,4767,0,0,0,209144,0,0,0.977207091765,1.0,0.988472169491