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 Mapped8700087.0%
Wrongly Mapped34393.439%
Not Mapped95619.561%
Total100000100.0%
Read Failure Statistics
Not mapped95329.532%
Missing in mapper output290.029%
Mapped to wrong chromosome00.0%
Mapped to wrong position34393.439%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment106
Secondary Alignments0
F-Measure0.930600
Precision0.962000
Recall0.901300
Timing
Raw Mapping Time120.964s
Effective Mapping Time120.924s
Effective Init Time0.040s
Effective Time MeasureCPU
Mapping Time (Wall)45.206s
Mapping Time (CPU)120.964s
Mapping Time (CPU User)118.428s
Mapping Time (CPU System)2.536s
Init Time (Wall)0.116s
Init Time (CPU)0.040s
Init Time (CPU User)0.008s
Init Time (CPU System)0.032s
Additional Information
Mapper Memory Usage142 MB
Total Test Runtime (Wall)70.310s
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
memory18652000
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: 0.064 sec; CPU: 0.020 sec
systime0.024
time0.101225137711
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/30952ba36f06792420203f74b83db277

/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
memory18652000
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: 0.078 sec; CPU: 0.032 sec
systime0.032
time0.115700960159
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/30952ba36f06792420203f74b83db277

/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
memory142200000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 100000 sequences/pairs (15540715 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: 45.159 sec; CPU: 120.936 sec
systime2.536
time45.2064950466
usrtime118.428
working_directory/project/teaser/genometeaser/tests_generated/30952ba36f06792420203f74b83db277