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 Mapped30072895.86%
Wrongly Mapped129874.14%
Not Mapped10.0%
Total313716100.0%
Read Failure Statistics
Not mapped10.0%
Missing in mapper output00.0%
Mapped to wrong chromosome93452.979%
Mapped to wrong position36421.161%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.978900
Precision0.958600
Recall1.000000
Timing
Raw Mapping Time2987.788s
Effective Mapping Time2986.384s
Effective Init Time1.404s
Effective Time MeasureCPU
Mapping Time (Wall)727.787s
Mapping Time (CPU)2987.788s
Mapping Time (CPU User)2978.032s
Mapping Time (CPU System)9.756s
Init Time (Wall)1.760s
Init Time (CPU)1.404s
Init Time (CPU User)0.600s
Init Time (CPU System)0.804s
Additional Information
Mapper Memory Usage2884 MB
Total Test Runtime (Wall)1026.525s
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
memory2878932000
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
systime1.916
time250.529546022
usrtime0.732
working_directory/project/teaser/genometeaser/tests_generated/6996f5893fc23a4f84e9e00364871d38

/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
memory2878160000
return1
status1
stderr
None
stdout

stampy: Error: File out_stampy.sam exists
systime0.804
time1.75981688499
usrtime0.6
working_directory/project/teaser/genometeaser/tests_generated/6996f5893fc23a4f84e9e00364871d38

/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
memory2884132000
return0
status1
stderr
None
stdout
stampy: Mapping...
stampy: # Nucleotides (all/1/2): 31371600 15685800 15685800
stampy: # Variants: 128319 64235 64084
stampy: # Fraction: 0.0041 0.0041 0.0041
stampy: # Paired-end insert size: 99.1 +/- 32.3 (153472 pairs)
stampy: Done
systime9.756
time727.787369013
usrtime2978.032
working_directory/project/teaser/genometeaser/tests_generated/6996f5893fc23a4f84e9e00364871d38