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 Mapped29461298.204%
Wrongly Mapped50361.679%
Not Mapped3520.117%
Total300000100.0%
Read Failure Statistics
Not mapped3520.117%
Missing in mapper output00.0%
Mapped to wrong chromosome40721.357%
Mapped to wrong position9640.321%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.990900
Precision0.983200
Recall0.998800
Timing
Raw Mapping Time13.448s
Effective Mapping Time13.400s
Effective Init Time0.048s
Effective Time MeasureCPU
Mapping Time (Wall)8.326s
Mapping Time (CPU)13.448s
Mapping Time (CPU User)12.560s
Mapping Time (CPU System)0.888s
Init Time (Wall)0.102s
Init Time (CPU)0.048s
Init Time (CPU User)0.008s
Init Time (CPU System)0.040s
Additional Information
Mapper Memory Usage179 MB
Total Test Runtime (Wall)42.593s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta 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/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory48832000
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 0.004 CPU sec, 0.002 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.066 sec; CPU: 0.040 sec
systime0.044
time0.0872640609741
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory48832000
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 0.000 CPU sec, 0.001 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.071 sec; CPU: 0.040 sec
systime0.04
time0.102397918701
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq -t 4 > out_bwamem.sam
memory179656000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 300000 sequences (15000000 bp)...
[M::mem_process_seqs] Processed 300000 reads in 12.964 CPU sec, 3.316 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq
[main] Real time: 8.291 sec; CPU: 13.440 sec
systime0.888
time8.32620096207
usrtime12.56
working_directory/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a