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 Mapped9632796.327%
Wrongly Mapped36623.662%
Not Mapped110.011%
Total100000100.0%
Read Failure Statistics
Not mapped110.011%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position36623.662%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.981300
Precision0.963400
Recall0.999900
Timing
Raw Mapping Time61.192s
Effective Mapping Time61.152s
Effective Init Time0.040s
Effective Time MeasureCPU
Mapping Time (Wall)28.189s
Mapping Time (CPU)61.192s
Mapping Time (CPU User)60.144s
Mapping Time (CPU System)1.048s
Init Time (Wall)0.445s
Init Time (CPU)0.040s
Init Time (CPU User)0.004s
Init Time (CPU System)0.036s
Additional Information
Mapper Memory Usage118 MB
Total Test Runtime (Wall)53.429s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.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/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory18652000
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, 0.060 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq
[main] Real time: 0.145 sec; CPU: 0.040 sec
systime0.04
time0.172350883484
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/30952ba36f06792420203f74b83db277

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory18652000
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 0.008 CPU sec, 0.036 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq
[main] Real time: 0.099 sec; CPU: 0.036 sec
systime0.036
time0.445261001587
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/30952ba36f06792420203f74b83db277

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads.fastq -t 4 > out_bwamem.sam
memory118576000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 100000 sequences (15540715 bp)...
[M::mem_process_seqs] Processed 100000 reads in 60.184 CPU sec, 20.672 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads.fastq
[main] Real time: 28.127 sec; CPU: 61.168 sec
systime1.048
time28.1888599396
usrtime60.144
working_directory/project/teaser/genometeaser/tests_generated/30952ba36f06792420203f74b83db277