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 Mapped47062590.01%
Wrongly Mapped323906.195%
Not Mapped198453.795%
Total522860100.0%
Read Failure Statistics
Not mapped198453.795%
Missing in mapper output00.0%
Mapped to wrong chromosome245784.701%
Mapped to wrong position78121.494%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment46
Secondary Alignments0
F-Measure0.947400
Precision0.935600
Recall0.959500
Timing
Raw Mapping Time220.240s
Effective Mapping Time215.788s
Effective Init Time4.452s
Effective Time MeasureCPU
Mapping Time (Wall)90.495s
Mapping Time (CPU)220.240s
Mapping Time (CPU User)204.772s
Mapping Time (CPU System)15.468s
Init Time (Wall)4.539s
Init Time (CPU)4.452s
Init Time (CPU User)0.140s
Init Time (CPU System)4.312s
Additional Information
Mapper Memory Usage5750 MB
Total Test Runtime (Wall)163.543s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa 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/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5366548000
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/H_sapiens.fa reads_base.fastq
[main] Real time: 4.505 sec; CPU: 4.420 sec
systime4.356
time4.53555297852
usrtime0.08
working_directory/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5365036000
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/H_sapiens.fa reads_base.fastq
[main] Real time: 4.499 sec; CPU: 4.436 sec
systime4.312
time4.53878688812
usrtime0.14
working_directory/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq -t 4 > out_bwasw.sam
memory5750912000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 522860 sequences/pairs (31371600 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq
[main] Real time: 90.447 sec; CPU: 220.224 sec
systime15.468
time90.4947068691
usrtime204.772
working_directory/project/teaser/genometeaser/tests_generated/73b7a31da9ec873be5a7818478a53cf8