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 Mapped32289389.864%
Wrongly Mapped3621210.078%
Not Mapped2090.058%
Total359314100.0%
Read Failure Statistics
Not mapped2090.058%
Missing in mapper output00.0%
Mapped to wrong chromosome210615.861%
Mapped to wrong position151514.217%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment41
Secondary Alignments0
F-Measure0.946600
Precision0.899200
Recall0.999400
Timing
Raw Mapping Time215.104s
Effective Mapping Time214.828s
Effective Init Time0.276s
Effective Time MeasureCPU
Mapping Time (Wall)83.868s
Mapping Time (CPU)215.104s
Mapping Time (CPU User)208.540s
Mapping Time (CPU System)6.564s
Init Time (Wall)0.404s
Init Time (CPU)0.276s
Init Time (CPU User)0.020s
Init Time (CPU System)0.256s
Additional Information
Mapper Memory Usage632 MB
Total Test Runtime (Wall)143.889s
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
memory248780000
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: 0.264 sec; CPU: 0.220 sec
systime0.224
time0.286554098129
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c

/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
memory250316000
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: 0.351 sec; CPU: 0.264 sec
systime0.256
time0.404089927673
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c

/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
memory632932000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 359314 sequences/pairs (35931400 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: 83.226 sec; CPU: 215.096 sec
systime6.564
time83.8680679798
usrtime208.54
working_directory/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c