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 Mapped58711774.86%
Wrongly Mapped525376.699%
Not Mapped14463618.442%
Total784290100.0%
Read Failure Statistics
Not mapped14463618.442%
Missing in mapper output00.0%
Mapped to wrong chromosome388524.954%
Mapped to wrong position136851.745%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.856200
Precision0.917900
Recall0.802300
Timing
Raw Mapping Time158.504s
Effective Mapping Time155.824s
Effective Init Time2.680s
Effective Time MeasureCPU
Mapping Time (Wall)109.484s
Mapping Time (CPU)158.504s
Mapping Time (CPU User)152.908s
Mapping Time (CPU System)5.596s
Init Time (Wall)2.749s
Init Time (CPU)2.680s
Init Time (CPU User)0.012s
Init Time (CPU System)2.668s
Additional Information
Mapper Memory Usage3309 MB
Total Test Runtime (Wall)411.865s
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
memory2336136000
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
systime4.68
time203.661782026
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa

/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
memory2336136000
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
systime2.668
time2.74862003326
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa

/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
memory3309032000
return0
status1
stderr
None
stdout
Warning: Exhausted best-first chunk memory for read read.000000100/1 (patid 100); skipping read
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Warning: Exhausted best-first chunk memory for read read.000080523/1 (patid 80523); skipping read
Warning: Exhausted
systime5.596
time109.484313965
usrtime152.908
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa