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 Mapped23590594.362%
Wrongly Mapped95153.806%
Not Mapped45801.832%
Total250000100.0%
Read Failure Statistics
Not mapped45801.832%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position95153.806%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment21
Secondary Alignments0
F-Measure0.971000
Precision0.961200
Recall0.981000
Timing
Raw Mapping Time75.124s
Effective Mapping Time75.088s
Effective Init Time0.036s
Effective Time MeasureCPU
Mapping Time (Wall)38.122s
Mapping Time (CPU)75.124s
Mapping Time (CPU User)71.480s
Mapping Time (CPU System)3.644s
Init Time (Wall)0.088s
Init Time (CPU)0.036s
Init Time (CPU User)0.008s
Init Time (CPU System)0.028s
Additional Information
Mapper Memory Usage196 MB
Total Test Runtime (Wall)69.718s
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
memory25616000
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: 0.052 sec; CPU: 0.024 sec
systime0.024
time0.0746240615845
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f

/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
memory25616000
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: 0.028 sec
systime0.028
time0.0884711742401
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f

/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
memory196256000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 250000 sequences/pairs (15000000 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: 38.085 sec; CPU: 75.100 sec
systime3.644
time38.1224198341
usrtime71.48
working_directory/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f