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 Mapped00.0%
Wrongly Mapped00.0%
Not Mapped149993100.0%
Total149993100.0%
Read Failure Statistics
Not mapped149993100.0%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position00.0%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment7
Secondary Alignments0
F-Measure0.000000
Precision0.000000
Recall0.000000
Timing
Raw Mapping Time1150.536s
Effective Mapping Time1150.292s
Effective Init Time0.244s
Effective Time MeasureCPU
Mapping Time (Wall)296.478s
Mapping Time (CPU)1150.536s
Mapping Time (CPU User)1126.192s
Mapping Time (CPU System)24.344s
Init Time (Wall)0.577s
Init Time (CPU)0.244s
Init Time (CPU User)0.164s
Init Time (CPU System)0.080s
Additional Information
Mapper Memory Usage38 MB
Total Test Runtime (Wall)332.211s
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
memory38176000
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
systime0.22
time2.35240387917
usrtime0.4
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923

/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
memory38176000
return1
status1
stderr
None
stdout

stampy: Error: File out_stampy.sam exists
systime0.08
time0.576900959015
usrtime0.164
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923

/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
memory38176000
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
systime24.344
time296.47754693
usrtime1126.192
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923