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 Mapped51591586.15%
Wrongly Mapped6753511.277%
Not Mapped154082.573%
Total598858100.0%
Read Failure Statistics
Not mapped154082.573%
Missing in mapper output00.0%
Mapped to wrong chromosome417606.973%
Mapped to wrong position257754.304%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment19
Secondary Alignments0
F-Measure0.925600
Precision0.884200
Recall0.971000
Timing
Raw Mapping Time319.472s
Effective Mapping Time318.724s
Effective Init Time0.748s
Effective Time MeasureCPU
Mapping Time (Wall)141.673s
Mapping Time (CPU)319.472s
Mapping Time (CPU User)305.144s
Mapping Time (CPU System)14.328s
Init Time (Wall)0.870s
Init Time (CPU)0.748s
Init Time (CPU User)0.024s
Init Time (CPU System)0.724s
Additional Information
Mapper Memory Usage686 MB
Total Test Runtime (Wall)238.533s
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
memory248776000
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: 1.814 sec; CPU: 1.044 sec
systime1.072
time1.86840391159
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/c474138b0d14daeadd1924f6eed36587

/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
memory248776000
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: 0.856 sec; CPU: 0.724 sec
systime0.724
time0.869944095612
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/c474138b0d14daeadd1924f6eed36587

/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
memory686520000
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: 141.598 sec; CPU: 319.376 sec
systime14.328
time141.672646999
usrtime305.144
working_directory/project/teaser/genometeaser/tests_generated/c474138b0d14daeadd1924f6eed36587