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 Mapped32323290.858%
Wrongly Mapped325249.142%
Not Mapped00.0%
Total355756100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome184465.185%
Mapped to wrong position140783.957%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.952100
Precision0.908600
Recall1.000000
Timing
Raw Mapping Time1248.792s
Effective Mapping Time1248.336s
Effective Init Time0.456s
Effective Time MeasureCPU
Mapping Time (Wall)296.893s
Mapping Time (CPU)1248.792s
Mapping Time (CPU User)1242.528s
Mapping Time (CPU System)6.264s
Init Time (Wall)0.637s
Init Time (CPU)0.456s
Init Time (CPU User)0.288s
Init Time (CPU System)0.168s
Additional Information
Mapper Memory Usage319 MB
Total Test Runtime (Wall)377.677s
Mapper Command Line: 
/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/D_melanogaster.fasta_o -h /project/teaser/genometeaser/references/D_melanogaster.fasta_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/D_melanogaster.fasta_o -h /project/teaser/genometeaser/references/D_melanogaster.fasta_o -M reads_base.fastq -o out_stampy.sam

command/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/D_melanogaster.fasta_o -h /project/teaser/genometeaser/references/D_melanogaster.fasta_o -M reads_base.fastq -o out_stampy.sam
memory314476000
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
systime0.444
time27.0857338905
usrtime0.452
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517

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

command/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/D_melanogaster.fasta_o -h /project/teaser/genometeaser/references/D_melanogaster.fasta_o -M reads_base.fastq -o out_stampy.sam
memory313708000
return1
status1
stderr
None
stdout

stampy: Error: File out_stampy.sam exists
systime0.168
time0.636571884155
usrtime0.288
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517

/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/D_melanogaster.fasta_o -h /project/teaser/genometeaser/references/D_melanogaster.fasta_o -o out_stampy.sam -M reads1.fastq reads2.fastq

command/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/D_melanogaster.fasta_o -h /project/teaser/genometeaser/references/D_melanogaster.fasta_o -o out_stampy.sam -M reads1.fastq reads2.fastq
memory319620000
return0
status1
stderr
None
stdout
stampy: Mapping...
stampy: # Nucleotides (all/1/2): 35931356 17965678 17965678
stampy: # Variants: 134158 66894 67264
stampy: # Fraction: 0.0037 0.0037 0.0037
stampy: # Paired-end insert size: 99.0 +/- 32.2 (169560 pairs)
stampy: Done
systime6.264
time296.893032074
usrtime1242.528
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517