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 Mapped51441585.899%
Wrongly Mapped6916911.55%
Not Mapped152742.551%
Total598858100.0%
Read Failure Statistics
Not mapped152742.551%
Missing in mapper output00.0%
Mapped to wrong chromosome426807.127%
Mapped to wrong position264894.423%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment25
Secondary Alignments0
F-Measure0.924100
Precision0.881500
Recall0.971200
Timing
Raw Mapping Time261.180s
Effective Mapping Time257.020s
Effective Init Time4.160s
Effective Time MeasureCPU
Mapping Time (Wall)93.908s
Mapping Time (CPU)261.180s
Mapping Time (CPU User)240.792s
Mapping Time (CPU System)20.388s
Init Time (Wall)4.287s
Init Time (CPU)4.160s
Init Time (CPU User)0.016s
Init Time (CPU System)4.144s
Additional Information
Mapper Memory Usage684 MB
Total Test Runtime (Wall)154.047s
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
memory248992000
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: 3.264 sec; CPU: 3.152 sec
systime3.164
time3.28708291054
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/370d4fd7160225b686abe184c6e4adf0

/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
memory248996000
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: 4.259 sec; CPU: 4.144 sec
systime4.144
time4.28732204437
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/370d4fd7160225b686abe184c6e4adf0

/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
memory684736000
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: 93.848 sec; CPU: 261.140 sec
systime20.388
time93.9080331326
usrtime240.792
working_directory/project/teaser/genometeaser/tests_generated/370d4fd7160225b686abe184c6e4adf0