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 Mapped40078095.814%
Wrongly Mapped175054.185%
Not Mapped30.001%
Total418288100.0%
Read Failure Statistics
Not mapped30.001%
Missing in mapper output00.0%
Mapped to wrong chromosome123852.961%
Mapped to wrong position51201.224%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.978600
Precision0.958200
Recall1.000000
Timing
Raw Mapping Time2405.568s
Effective Mapping Time2403.768s
Effective Init Time1.800s
Effective Time MeasureCPU
Mapping Time (Wall)578.654s
Mapping Time (CPU)2405.568s
Mapping Time (CPU User)2395.184s
Mapping Time (CPU System)10.384s
Init Time (Wall)2.153s
Init Time (CPU)1.800s
Init Time (CPU User)0.612s
Init Time (CPU System)1.188s
Additional Information
Mapper Memory Usage2883 MB
Total Test Runtime (Wall)886.806s
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
memory2879004000
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
systime2.24
time251.859585047
usrtime0.892
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1

/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
memory2878092000
return1
status1
stderr
None
stdout

stampy: Error: File out_stampy.sam exists
systime1.188
time2.15341687202
usrtime0.612
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1

/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
memory2883860000
return0
status1
stderr
None
stdout
stampy: Mapping...
stampy: # Nucleotides (all/1/2): 31371450 15685725 15685725
stampy: # Variants: 128728 64058 64670
stampy: # Fraction: 0.0041 0.0041 0.0041
stampy: # Paired-end insert size: 448.0 +/- 64.8 (202171 pairs)
stampy: Done
systime10.384
time578.653879881
usrtime2395.184
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1