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 Mapped11045973.639%
Wrongly Mapped41362.757%
Not Mapped3540523.603%
Total150000100.0%
Read Failure Statistics
Not mapped3540123.601%
Missing in mapper output40.003%
Mapped to wrong chromosome00.0%
Mapped to wrong position41362.757%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment42
Secondary Alignments0
F-Measure0.848200
Precision0.963900
Recall0.757300
Timing
Raw Mapping Time87.372s
Effective Mapping Time87.332s
Effective Init Time0.040s
Effective Time MeasureCPU
Mapping Time (Wall)37.364s
Mapping Time (CPU)87.372s
Mapping Time (CPU User)85.120s
Mapping Time (CPU System)2.252s
Init Time (Wall)0.148s
Init Time (CPU)0.040s
Init Time (CPU User)0.004s
Init Time (CPU System)0.036s
Additional Information
Mapper Memory Usage181 MB
Total Test Runtime (Wall)60.805s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta 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/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory21712000
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/E_coli.fasta reads_base.fastq
[main] Real time: 0.074 sec; CPU: 0.024 sec
systime0.028
time0.100422143936
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory21712000
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/E_coli.fasta reads_base.fastq
[main] Real time: 0.057 sec; CPU: 0.032 sec
systime0.036
time0.14822101593
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads.fastq -t 4 > out_bwasw.sam
memory181016000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 150000 sequences/pairs (15540421 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads.fastq
[main] Real time: 37.295 sec; CPU: 87.340 sec
systime2.252
time37.3635070324
usrtime85.12
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558