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 Mapped14449796.331%
Wrongly Mapped53333.555%
Not Mapped1700.113%
Total150000100.0%
Read Failure Statistics
Not mapped1700.113%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position53333.555%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.981300
Precision0.964400
Recall0.998800
Timing
Raw Mapping Time82.488s
Effective Mapping Time82.452s
Effective Init Time0.036s
Effective Time MeasureCPU
Mapping Time (Wall)42.642s
Mapping Time (CPU)82.488s
Mapping Time (CPU User)82.024s
Mapping Time (CPU System)0.464s
Init Time (Wall)0.399s
Init Time (CPU)0.036s
Init Time (CPU User)0.016s
Init Time (CPU System)0.020s
Additional Information
Mapper Memory Usage21 MB
Total Test Runtime (Wall)68.572s
Mapper Command Line: 
/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/E_coli.fasta_cushaw3 -f reads.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/E_coli.fasta_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/E_coli.fasta_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1
memory21712000
return0
status1
stderr
None
stdout
Command: align -r /project/teaser/genometeaser/references/E_coli.fasta_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1 
Suffix array memory size: 2.44716 MB
FASTQ format identified
#Reads aligned: 0 / 1 (0.00%)
Overall time: 1.06 seconds
systime0.032
time1.09757304192
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558

/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/E_coli.fasta_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/E_coli.fasta_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1
memory21712000
return0
status1
stderr
None
stdout
Command: align -r /project/teaser/genometeaser/references/E_coli.fasta_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1 
Suffix array memory size: 2.44716 MB
FASTQ format identified
#Reads aligned: 0 / 1 (0.00%)
Overall time: 0.10 seconds
systime0.02
time0.398652076721
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558

/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/E_coli.fasta_cushaw3 -f reads.fastq -o out_cushaw3.sam -t 4 -multi 1

command/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/E_coli.fasta_cushaw3 -f reads.fastq -o out_cushaw3.sam -t 4 -multi 1
memory21712000
return0
status1
stderr
None
stdout
Command: align -r /project/teaser/genometeaser/references/E_coli.fasta_cushaw3 -f reads.fastq -o out_cushaw3.sam -t 4 -multi 1 
Suffix array memory size: 2.44716 MB
FASTQ format identified
#Reads aligned: 149830 / 150000 (99.89%)
Overall time: 42.58 seconds
systime0.464
time42.6422069073
usrtime82.024
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558