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 Mapped29448898.163%
Wrongly Mapped51521.717%
Not Mapped3600.12%
Total300000100.0%
Read Failure Statistics
Not mapped3600.12%
Missing in mapper output00.0%
Mapped to wrong chromosome41751.392%
Mapped to wrong position9770.326%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.990700
Precision0.982800
Recall0.998800
Timing
Raw Mapping Time37.348s
Effective Mapping Time37.288s
Effective Init Time0.060s
Effective Time MeasureCPU
Mapping Time (Wall)27.947s
Mapping Time (CPU)37.348s
Mapping Time (CPU User)36.200s
Mapping Time (CPU System)1.148s
Init Time (Wall)0.367s
Init Time (CPU)0.060s
Init Time (CPU User)0.008s
Init Time (CPU System)0.052s
Additional Information
Mapper Memory Usage178 MB
Total Test Runtime (Wall)80.506s
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 0.000 CPU sec, 0.060 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: 0.201 sec; CPU: 0.060 sec
systime0.06
time0.236978054047
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972

/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, 0.033 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: 0.142 sec; CPU: 0.048 sec
systime0.052
time0.366780996323
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972

/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
memory178844000
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 36.488 CPU sec, 20.124 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: 27.880 sec; CPU: 37.300 sec
systime1.148
time27.9467718601
usrtime36.2
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972