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 Mapped5126724.513%
Wrongly Mapped14030.671%
Not Mapped15647474.816%
Total209144100.0%
Read Failure Statistics
Not mapped15647474.816%
Missing in mapper output00.0%
Mapped to wrong chromosome8420.403%
Mapped to wrong position5610.268%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.393700
Precision0.973400
Recall0.246800
Timing
Raw Mapping Time151.608s
Effective Mapping Time148.960s
Effective Init Time2.648s
Effective Time MeasureCPU
Mapping Time (Wall)102.508s
Mapping Time (CPU)151.608s
Mapping Time (CPU User)146.088s
Mapping Time (CPU System)5.520s
Init Time (Wall)2.729s
Init Time (CPU)2.648s
Init Time (CPU User)0.004s
Init Time (CPU System)2.644s
Additional Information
Mapper Memory Usage3309 MB
Total Test Runtime (Wall)353.590s
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
memory2336140000
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
systime3.812
time203.412999153
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

/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
memory2336228000
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
systime2.644
time2.7286529541
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

/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
memory3309292000
return0
status1
stderr
None
stdout
Warning: Exhausted best-first chunk memory for read read.000000164/1 (patid 164); skipping read
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Warning: Exhausted best-first chunk memory for read read.000010437/1 (patid 10437); skipping read
Warning: Exh
systime5.52
time102.508263111
usrtime146.088
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12