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 Mapped29440398.134%
Wrongly Mapped52311.744%
Not Mapped3660.122%
Total300000100.0%
Read Failure Statistics
Not mapped3660.122%
Missing in mapper output00.0%
Mapped to wrong chromosome42471.416%
Mapped to wrong position9840.328%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.990600
Precision0.982500
Recall0.998800
Timing
Raw Mapping Time46.508s
Effective Mapping Time46.432s
Effective Init Time0.076s
Effective Time MeasureCPU
Mapping Time (Wall)31.481s
Mapping Time (CPU)46.508s
Mapping Time (CPU User)44.992s
Mapping Time (CPU System)1.516s
Init Time (Wall)7.664s
Init Time (CPU)0.076s
Init Time (CPU User)0.024s
Init Time (CPU System)0.052s
Additional Information
Mapper Memory Usage176 MB
Total Test Runtime (Wall)99.778s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.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/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory48836000
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 0.004 CPU sec, 0.041 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.132 sec; CPU: 0.044 sec
systime0.052
time0.167850971222
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory48836000
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 0.008 CPU sec, 0.048 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 4.716 sec; CPU: 0.064 sec
systime0.052
time7.66443705559
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq -t 4 > out_bwamem.sam
memory176740000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 300000 sequences (15000000 bp)...
[M::mem_process_seqs] Processed 300000 reads in 45.232 CPU sec, 23.127 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq
[main] Real time: 31.382 sec; CPU: 46.448 sec
systime1.516
time31.4811558723
usrtime44.992
working_directory/project/teaser/genometeaser/tests_generated/316281ab4f84058f3c27332d7303df8f