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 Mapped65803575.512%
Wrongly Mapped516815.931%
Not Mapped16171618.558%
Total871432100.0%
Read Failure Statistics
Not mapped16171618.558%
Missing in mapper output00.0%
Mapped to wrong chromosome376964.326%
Mapped to wrong position139851.605%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.860500
Precision0.927200
Recall0.802700
Timing
Raw Mapping Time197.544s
Effective Mapping Time195.032s
Effective Init Time2.512s
Effective Time MeasureCPU
Mapping Time (Wall)117.097s
Mapping Time (CPU)197.544s
Mapping Time (CPU User)191.700s
Mapping Time (CPU System)5.844s
Init Time (Wall)2.581s
Init Time (CPU)2.512s
Init Time (CPU User)0.004s
Init Time (CPU System)2.508s
Additional Information
Mapper Memory Usage3305 MB
Total Test Runtime (Wall)453.978s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo -1 reads1.fastq -2 reads2.fastq out_bowtie.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads_base.fastq out_bowtie.sam

command/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads_base.fastq out_bowtie.sam
memory2336236000
return0
status1
stderr
None
stdout
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments
systime3.092
time203.42115593
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf

/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads_base.fastq out_bowtie.sam

command/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads_base.fastq out_bowtie.sam
memory2336216000
return0
status1
stderr
None
stdout
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments
systime2.508
time2.58125901222
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf

/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo -1 reads1.fastq -2 reads2.fastq out_bowtie.sam

command/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo -1 reads1.fastq -2 reads2.fastq out_bowtie.sam
memory3305076000
return0
status1
stderr
None
stdout
Warning: Exhausted best-first chunk memory for read read.000007095/1 (patid 7095); skipping read
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Warning: Exhausted best-first chunk memory for read read.000170562
systime5.844
time117.09736681
usrtime191.7
working_directory/project/teaser/genometeaser/tests_generated/ab0014cf05e86cd590ae0b3283410abf