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 Mapped64278073.761%
Wrongly Mapped9533710.94%
Not Mapped13331615.298%
Total871433100.0%
Read Failure Statistics
Not mapped13331615.298%
Missing in mapper output00.0%
Mapped to wrong chromosome801809.201%
Mapped to wrong position151531.739%
Mapped to wrong strand40.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.849000
Precision0.870800
Recall0.828200
Timing
Raw Mapping Time215.668s
Effective Mapping Time181.544s
Effective Init Time34.124s
Effective Time MeasureCPU
Mapping Time (Wall)83.319s
Mapping Time (CPU)215.668s
Mapping Time (CPU User)156.676s
Mapping Time (CPU System)58.992s
Init Time (Wall)34.221s
Init Time (CPU)34.124s
Init Time (CPU User)0.036s
Init Time (CPU System)34.088s
Additional Information
Mapper Memory Usage5915 MB
Total Test Runtime (Wall)191.393s
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
memory5365200000
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: 36.182 sec; CPU: 36.008 sec
systime35.956
time36.2034609318
usrtime0.064
working_directory/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d

/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
memory5365156000
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: 34.196 sec; CPU: 34.112 sec
systime34.088
time34.2207551003
usrtime0.036
working_directory/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d

/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
memory5915688000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 871433 sequences/pairs (31371588 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: 83.259 sec; CPU: 215.624 sec
systime58.992
time83.3190639019
usrtime156.676
working_directory/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d