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 Mapped58607674.727%
Wrongly Mapped760509.697%
Not Mapped12216415.576%
Total784290100.0%
Read Failure Statistics
Not mapped12216415.576%
Missing in mapper output00.0%
Mapped to wrong chromosome631308.049%
Mapped to wrong position129181.647%
Mapped to wrong strand20.0%
Advanced Statistics
Missing in comparison alignment1
Secondary Alignments0
F-Measure0.855400
Precision0.885100
Recall0.827500
Timing
Raw Mapping Time163.888s
Effective Mapping Time159.096s
Effective Init Time4.792s
Effective Time MeasureCPU
Mapping Time (Wall)62.049s
Mapping Time (CPU)163.888s
Mapping Time (CPU User)151.304s
Mapping Time (CPU System)12.584s
Init Time (Wall)4.890s
Init Time (CPU)4.792s
Init Time (CPU User)0.120s
Init Time (CPU System)4.672s
Additional Information
Mapper Memory Usage5884 MB
Total Test Runtime (Wall)144.254s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5365024000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.865 sec; CPU: 4.784 sec
systime4.696
time4.89719295502
usrtime0.112
working_directory/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5364904000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.848 sec; CPU: 4.772 sec
systime4.672
time4.89019203186
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq -t 4 > out_bwasw.sam
memory5884980000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 784290 sequences/pairs (31371600 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq
[main] Real time: 61.990 sec; CPU: 163.864 sec
systime12.584
time62.0491890907
usrtime151.304
working_directory/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f