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 Mapped51520786.032%
Wrongly Mapped6834011.412%
Not Mapped153112.557%
Total598858100.0%
Read Failure Statistics
Not mapped153112.557%
Missing in mapper output00.0%
Mapped to wrong chromosome423787.076%
Mapped to wrong position259624.335%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment28
Secondary Alignments0
F-Measure0.924900
Precision0.882900
Recall0.971100
Timing
Raw Mapping Time185.860s
Effective Mapping Time185.608s
Effective Init Time0.252s
Effective Time MeasureCPU
Mapping Time (Wall)67.998s
Mapping Time (CPU)185.860s
Mapping Time (CPU User)177.340s
Mapping Time (CPU System)8.520s
Init Time (Wall)0.341s
Init Time (CPU)0.252s
Init Time (CPU User)0.020s
Init Time (CPU System)0.232s
Additional Information
Mapper Memory Usage686 MB
Total Test Runtime (Wall)111.980s
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
memory248904000
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: 0.266 sec; CPU: 0.232 sec
systime0.232
time0.287197113037
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/63224990d2f5aeaa3b674d6cbc4acc8f

/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
memory250356000
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: 0.313 sec; CPU: 0.232 sec
systime0.232
time0.340620040894
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/63224990d2f5aeaa3b674d6cbc4acc8f

/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
memory686432000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 67.948 sec; CPU: 185.816 sec
systime8.52
time67.9982089996
usrtime177.34
working_directory/project/teaser/genometeaser/tests_generated/63224990d2f5aeaa3b674d6cbc4acc8f