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 Mapped3237297.117%
Wrongly Mapped9612.883%
Not Mapped00.0%
Total33333100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position9612.883%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment6
Secondary Alignments0
F-Measure0.985400
Precision0.971200
Recall1.000000
Timing
Raw Mapping Time65.608s
Effective Mapping Time65.572s
Effective Init Time0.036s
Effective Time MeasureCPU
Mapping Time (Wall)32.377s
Mapping Time (CPU)65.608s
Mapping Time (CPU User)64.844s
Mapping Time (CPU System)0.764s
Init Time (Wall)0.089s
Init Time (CPU)0.036s
Init Time (CPU User)0.008s
Init Time (CPU System)0.028s
Additional Information
Mapper Memory Usage122 MB
Total Test Runtime (Wall)49.316s
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
memory14340000
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: 0.050 sec; CPU: 0.024 sec
systime0.032
time0.0761098861694
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e

/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
memory15064000
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: 0.066 sec; CPU: 0.028 sec
systime0.028
time0.0885438919067
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e

/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
memory122896000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 33333 sequences/pairs (14999850 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: 32.345 sec; CPU: 65.600 sec
systime0.764
time32.3770608902
usrtime64.844
working_directory/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e