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 Mapped66022173.498%
Wrongly Mapped10050311.188%
Not Mapped13756315.314%
Total898287100.0%
Read Failure Statistics
Not mapped13756315.314%
Missing in mapper output00.0%
Mapped to wrong chromosome658607.332%
Mapped to wrong position346433.857%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment1
Secondary Alignments0
F-Measure0.847200
Precision0.867900
Recall0.827600
Timing
Raw Mapping Time171.272s
Effective Mapping Time170.988s
Effective Init Time0.284s
Effective Time MeasureCPU
Mapping Time (Wall)62.805s
Mapping Time (CPU)171.272s
Mapping Time (CPU User)159.504s
Mapping Time (CPU System)11.768s
Init Time (Wall)0.366s
Init Time (CPU)0.284s
Init Time (CPU User)0.016s
Init Time (CPU System)0.268s
Additional Information
Mapper Memory Usage844 MB
Total Test Runtime (Wall)130.431s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory322468000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.316 sec; CPU: 0.264 sec
systime0.268
time0.354496002197
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory322468000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.319 sec; CPU: 0.268 sec
systime0.268
time0.365895032883
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwasw.sam
memory844360000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 898287 sequences/pairs (35931480 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 62.741 sec; CPU: 171.212 sec
systime11.768
time62.804598093
usrtime159.504
working_directory/project/teaser/genometeaser/tests_generated/be9adfa40f58b4dfd03b6dd3624949ef