Mapping Quality Thresholds

The plot below shows the percentages of correctly and wrongly mapped reads for all mapping quality thresholds for this mapper. The values at threshold 0 therefore correspond to the unfiltered results.

Basic Statistics
Correctly Mapped20437797.721%
Wrongly Mapped47672.279%
Not Mapped00.0%
Total209144100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome31111.487%
Mapped to wrong position16560.792%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.988500
Precision0.977200
Recall1.000000
Timing
Raw Mapping Time3512.056s
Effective Mapping Time3510.876s
Effective Init Time1.180s
Effective Time MeasureCPU
Mapping Time (Wall)860.640s
Mapping Time (CPU)3512.056s
Mapping Time (CPU User)3500.572s
Mapping Time (CPU System)11.484s
Init Time (Wall)1.346s
Init Time (CPU)1.180s
Init Time (CPU User)0.652s
Init Time (CPU System)0.528s
Additional Information
Mapper Memory Usage2885 MB
Total Test Runtime (Wall)899.544s
Mapper Command Line: 
/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
Errors and Warnings
No problems were encountered.
Subprocess Log

/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

command/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
memory2878936000
return0
status1
stderr
None
stdout
stampy: Mapping...
stampy: # Nucleotides (all/1/2): 0 0 0
stampy: # Variants: 0 0 0
stampy: # Fraction: 0.0000 0.0000 0.0000
stampy: Done
systime0.668
time1.86851000786
usrtime0.812
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

/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

command/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
memory2878136000
return1
status1
stderr
None
stdout

stampy: Error: File out_stampy.sam exists
systime0.528
time1.34570789337
usrtime0.652
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

/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

command/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
memory2885012000
return0
status1
stderr
None
stdout
stampy: Mapping...
stampy: # Nucleotides (all/1/2): 31371600 15685800 15685800
stampy: # Variants: 117867 59053 58814
stampy: # Fraction: 0.0038 0.0038 0.0037
stampy: # Paired-end insert size: 248.4 +/- 32.6 (103678 pairs)
stampy: Done
systime11.484
time860.640367985
usrtime3500.572
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12