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 Mapped52915588.361%
Wrongly Mapped6960511.623%
Not Mapped980.016%
Total598858100.0%
Read Failure Statistics
Not mapped980.016%
Missing in mapper output00.0%
Mapped to wrong chromosome412596.89%
Mapped to wrong position283464.733%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.938200
Precision0.883800
Recall0.999800
Timing
Raw Mapping Time66.393s
Effective Mapping Time66.244s
Effective Init Time0.149s
Effective Time MeasureCPU
Mapping Time (Wall)18.581s
Mapping Time (CPU)66.393s
Mapping Time (CPU User)65.565s
Mapping Time (CPU System)0.828s
Init Time (Wall)0.187s
Init Time (CPU)0.149s
Init Time (CPU User)0.006s
Init Time (CPU System)0.143s
Additional Information
Mapper Memory Usage938 MB
Total Test Runtime (Wall)43.154s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory247132000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.001 CPU sec, 0.001 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.177 sec; CPU: 0.141 sec
systime0.139978
time0.182343006134
usrtime0.005999
working_directory/project/teaser/genometeaser/tests_generated/465464d523f5a7eb9d2d48753a117599

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory247136000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (60 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.002 CPU sec, 0.001 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.181 sec; CPU: 0.144 sec
systime0.142978
time0.186714887619
usrtime0.005999
working_directory/project/teaser/genometeaser/tests_generated/465464d523f5a7eb9d2d48753a117599

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwamem.sam
memory938328000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 598858 sequences (35931480 bp)...
[M::mem_process_seqs] Processed 598858 reads in 65.683 CPU sec, 16.505 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 18.568 sec; CPU: 66.379 sec
systime0.827874
time18.5811100006
usrtime65.565032
working_directory/project/teaser/genometeaser/tests_generated/465464d523f5a7eb9d2d48753a117599