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 Mapped20473397.891%
Wrongly Mapped44112.109%
Not Mapped00.0%
Total209144100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome27521.316%
Mapped to wrong position16590.793%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.989300
Precision0.978900
Recall1.000000
Timing
Raw Mapping Time394.832s
Effective Mapping Time391.152s
Effective Init Time3.680s
Effective Time MeasureCPU
Mapping Time (Wall)103.181s
Mapping Time (CPU)394.832s
Mapping Time (CPU User)386.692s
Mapping Time (CPU System)8.140s
Init Time (Wall)3.824s
Init Time (CPU)3.680s
Init Time (CPU User)0.008s
Init Time (CPU System)3.672s
Additional Information
Mapper Memory Usage3643 MB
Total Test Runtime (Wall)439.946s
Mapper Command Line: 
/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/H_sapiens.fa_cushaw3 -q reads1.fastq reads2.fastq -o out_cushaw3.sam -t 4 -multi 1
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/H_sapiens.fa_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1

command/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/H_sapiens.fa_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1
memory3449060000
return0
status1
stderr
None
stdout
Command: align -r /project/teaser/genometeaser/references/H_sapiens.fa_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1 
Suffix array memory size: 1495.92 MB
FASTQ format identified
#Reads aligned: 0 / 1 (0.00%)
Overall time: 300.29 seconds
systime5.94
time300.299405098
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/H_sapiens.fa_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1

command/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/H_sapiens.fa_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1
memory3449060000
return0
status1
stderr
None
stdout
Command: align -r /project/teaser/genometeaser/references/H_sapiens.fa_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1 
Suffix array memory size: 1495.92 MB
FASTQ format identified
#Reads aligned: 0 / 1 (0.00%)
Overall time: 3.80 seconds
systime3.672
time3.82442593575
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/H_sapiens.fa_cushaw3 -q reads1.fastq reads2.fastq -o out_cushaw3.sam -t 4 -multi 1

command/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/H_sapiens.fa_cushaw3 -q reads1.fastq reads2.fastq -o out_cushaw3.sam -t 4 -multi 1
memory3643476000
return0
status1
stderr
None
stdout
Command: align -r /project/teaser/genometeaser/references/H_sapiens.fa_cushaw3 -q reads1.fastq reads2.fastq -o out_cushaw3.sam -t 4 -multi 1 
Suffix array memory size: 1495.92 MB
Start estimating insert size using the top 0x10000 read pairs
FASTQ format identified
FASTQ format identified
#read pairs read from the input: 65536
Estimated insert size: 249 +/- 33 from 60965 effective samples
Finish estimating insert size (taken 33.227918 seconds using 4 threads)
FASTQ format identified
FASTQ format identified
#Reads aligned: 209144 / 209144 (100.00%)
#Reads paired: 209144 / 209144 (100.00%)
Overall time: 103.13 seconds
systime8.14
time103.180845022
usrtime386.692
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12