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 Mapped14462196.414%
Wrongly Mapped53473.565%
Not Mapped320.021%
Total150000100.0%
Read Failure Statistics
Not mapped320.021%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position53473.565%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.981700
Precision0.964300
Recall0.999800
Timing
Raw Mapping Time1788.692s
Effective Mapping Time1788.308s
Effective Init Time0.384s
Effective Time MeasureCPU
Mapping Time (Wall)471.279s
Mapping Time (CPU)1788.692s
Mapping Time (CPU User)1616.764s
Mapping Time (CPU System)171.928s
Init Time (Wall)1.174s
Init Time (CPU)0.384s
Init Time (CPU User)0.260s
Init Time (CPU System)0.124s
Additional Information
Mapper Memory Usage38 MB
Total Test Runtime (Wall)506.105s
Mapper Command Line: 
/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/E_coli.fasta_o -h /project/teaser/genometeaser/references/E_coli.fasta_o -M reads.fastq -o out_stampy.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/E_coli.fasta_o -h /project/teaser/genometeaser/references/E_coli.fasta_o -M reads_base.fastq -o out_stampy.sam

command/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/E_coli.fasta_o -h /project/teaser/genometeaser/references/E_coli.fasta_o -M reads_base.fastq -o out_stampy.sam
memory38188000
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
systime0.208
time1.15520691872
usrtime0.288
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558

/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/E_coli.fasta_o -h /project/teaser/genometeaser/references/E_coli.fasta_o -M reads_base.fastq -o out_stampy.sam

command/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/E_coli.fasta_o -h /project/teaser/genometeaser/references/E_coli.fasta_o -M reads_base.fastq -o out_stampy.sam
memory38188000
return1
status1
stderr
None
stdout

stampy: Error: File out_stampy.sam exists
systime0.124
time1.17396497726
usrtime0.26
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558

/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/E_coli.fasta_o -h /project/teaser/genometeaser/references/E_coli.fasta_o -M reads.fastq -o out_stampy.sam

command/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/E_coli.fasta_o -h /project/teaser/genometeaser/references/E_coli.fasta_o -M reads.fastq -o out_stampy.sam
memory38188000
return0
status1
stderr
None
stdout
stampy: Mapping...
stampy: # Nucleotides (all/1/2): 15536960 15536960 0
stampy: # Variants: 240170 240170 0
stampy: # Fraction: 0.0155 0.0155 0.0000
stampy: Done
systime171.928
time471.279223919
usrtime1616.764
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558