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 Mapped51357285.759%
Wrongly Mapped7002511.693%
Not Mapped152612.548%
Total598858100.0%
Read Failure Statistics
Not mapped152612.548%
Missing in mapper output00.0%
Mapped to wrong chromosome438687.325%
Mapped to wrong position261574.368%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment34
Secondary Alignments0
F-Measure0.923300
Precision0.880000
Recall0.971100
Timing
Raw Mapping Time230.860s
Effective Mapping Time230.560s
Effective Init Time0.300s
Effective Time MeasureCPU
Mapping Time (Wall)71.204s
Mapping Time (CPU)230.860s
Mapping Time (CPU User)221.928s
Mapping Time (CPU System)8.932s
Init Time (Wall)0.372s
Init Time (CPU)0.300s
Init Time (CPU User)0.012s
Init Time (CPU System)0.288s
Additional Information
Mapper Memory Usage685 MB
Total Test Runtime (Wall)113.928s
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: 0.318 sec; CPU: 0.256 sec
systime0.256
time0.34787106514
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8

/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
memory250448000
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: 0.341 sec; CPU: 0.284 sec
systime0.288
time0.372341156006
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8

/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
memory685332000
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: 71.140 sec; CPU: 230.808 sec
systime8.932
time71.2039740086
usrtime221.928
working_directory/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8