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 Mapped32392791.053%
Wrongly Mapped318298.947%
Not Mapped00.0%
Total355756100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome175044.92%
Mapped to wrong position143254.027%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.953200
Precision0.910500
Recall1.000000
Timing
Raw Mapping Time244.868s
Effective Mapping Time244.676s
Effective Init Time0.192s
Effective Time MeasureCPU
Mapping Time (Wall)65.936s
Mapping Time (CPU)244.868s
Mapping Time (CPU User)243.884s
Mapping Time (CPU System)0.984s
Init Time (Wall)0.249s
Init Time (CPU)0.192s
Init Time (CPU User)0.028s
Init Time (CPU System)0.164s
Additional Information
Mapper Memory Usage308 MB
Total Test Runtime (Wall)131.650s
Mapper Command Line: 
/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/D_melanogaster.fasta_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/D_melanogaster.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/D_melanogaster.fasta_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1
memory161972000
return0
status1
stderr
None
stdout
Command: align -r /project/teaser/genometeaser/references/D_melanogaster.fasta_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1 
Suffix array memory size: 68.5339 MB
FASTQ format identified
#Reads aligned: 0 / 1 (0.00%)
Overall time: 14.05 seconds
systime0.216
time14.0550968647
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517

/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/D_melanogaster.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/D_melanogaster.fasta_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1
memory161968000
return0
status1
stderr
None
stdout
Command: align -r /project/teaser/genometeaser/references/D_melanogaster.fasta_cushaw3 -f reads_base.fastq -o out_cushaw3.sam -t 4 -multi 1 
Suffix array memory size: 68.5339 MB
FASTQ format identified
#Reads aligned: 0 / 1 (0.00%)
Overall time: 0.23 seconds
systime0.164
time0.248878002167
usrtime0.028
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517

/project/teaser/genometeaser/software/cushaw3/cushaw3 align -r /project/teaser/genometeaser/references/D_melanogaster.fasta_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/D_melanogaster.fasta_cushaw3 -q reads1.fastq reads2.fastq -o out_cushaw3.sam -t 4 -multi 1
memory308220000
return0
status1
stderr
None
stdout
Command: align -r /project/teaser/genometeaser/references/D_melanogaster.fasta_cushaw3 -q reads1.fastq reads2.fastq -o out_cushaw3.sam -t 4 -multi 1 
Suffix array memory size: 68.5339 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: 100 +/- 20 from 55605 effective samples
Finish estimating insert size (taken 12.413512 seconds using 4 threads)
FASTQ format identified
FASTQ format identified
#Reads aligned: 355756 / 355756 (100.00%)
#Reads paired: 355756 / 355756 (100.00%)
Overall time: 65.90 seconds
systime0.984
time65.9357521534
usrtime243.884
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517