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 Mapped14622797.485%
Wrongly Mapped37712.514%
Not Mapped20.001%
Total150000100.0%
Read Failure Statistics
Not mapped20.001%
Missing in mapper output00.0%
Mapped to wrong chromosome18251.217%
Mapped to wrong position19461.297%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.987300
Precision0.974900
Recall1.000000
Timing
Raw Mapping Time14.823s
Effective Mapping Time14.804s
Effective Init Time0.019s
Effective Time MeasureCPU
Mapping Time (Wall)7.785s
Mapping Time (CPU)14.823s
Mapping Time (CPU User)14.580s
Mapping Time (CPU System)0.243s
Init Time (Wall)0.233s
Init Time (CPU)0.019s
Init Time (CPU User)0.000s
Init Time (CPU System)0.019s
Additional Information
Mapper Memory Usage149 MB
Total Test Runtime (Wall)22.055s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq -t 4 > out_bwamem.sam
memory22756000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.001 CPU sec, 0.001 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq
[main] Real time: 0.087 sec; CPU: 0.016 sec
systime0.015997
time0.0923910140991
usrtime0.002999
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq -t 4 > out_bwamem.sam
memory22756000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.001 CPU sec, 0.000 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq
[main] Real time: 0.059 sec; CPU: 0.017 sec
systime0.018997
time0.232692956924
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq -t 4 > out_bwamem.sam
memory149688000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 150000 sequences (15000000 bp)...
[M::mem_process_seqs] Processed 150000 reads in 14.609 CPU sec, 6.906 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq
[main] Real time: 7.778 sec; CPU: 14.818 sec
systime0.242963
time7.78519701958
usrtime14.579783
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157