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 Mapped51450185.914%
Wrongly Mapped6904311.529%
Not Mapped153142.557%
Total598858100.0%
Read Failure Statistics
Not mapped153142.557%
Missing in mapper output00.0%
Mapped to wrong chromosome428907.162%
Mapped to wrong position261524.367%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment35
Secondary Alignments0
F-Measure0.924200
Precision0.881700
Recall0.971100
Timing
Raw Mapping Time162.999s
Effective Mapping Time162.851s
Effective Init Time0.148s
Effective Time MeasureCPU
Mapping Time (Wall)43.630s
Mapping Time (CPU)162.999s
Mapping Time (CPU User)161.552s
Mapping Time (CPU System)1.447s
Init Time (Wall)0.310s
Init Time (CPU)0.148s
Init Time (CPU User)0.007s
Init Time (CPU System)0.141s
Additional Information
Mapper Memory Usage647 MB
Total Test Runtime (Wall)68.680s
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
memory247272000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.198 sec; CPU: 0.133 sec
systime0.133979
time0.204551935196
usrtime0.005999
working_directory/project/teaser/genometeaser/tests_generated/465464d523f5a7eb9d2d48753a117599

/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
memory247276000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.303 sec; CPU: 0.143 sec
systime0.140978
time0.309699058533
usrtime0.006998
working_directory/project/teaser/genometeaser/tests_generated/465464d523f5a7eb9d2d48753a117599

/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
memory647616000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 598858 sequences/pairs (35931480 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 43.618 sec; CPU: 162.989 sec
systime1.44678
time43.6303999424
usrtime161.55244
working_directory/project/teaser/genometeaser/tests_generated/465464d523f5a7eb9d2d48753a117599