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 Mapped14409396.062%
Wrongly Mapped52993.533%
Not Mapped6080.405%
Total150000100.0%
Read Failure Statistics
Not mapped6080.405%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position52993.533%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.979900
Precision0.964500
Recall0.995800
Timing
Raw Mapping Time33.676s
Effective Mapping Time33.648s
Effective Init Time0.028s
Effective Time MeasureCPU
Mapping Time (Wall)24.913s
Mapping Time (CPU)33.676s
Mapping Time (CPU User)32.864s
Mapping Time (CPU System)0.812s
Init Time (Wall)0.135s
Init Time (CPU)0.028s
Init Time (CPU User)0.000s
Init Time (CPU System)0.028s
Additional Information
Mapper Memory Usage150 MB
Total Test Runtime (Wall)50.854s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.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/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory21712000
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, 0.036 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq
[main] Real time: 0.134 sec; CPU: 0.036 sec
systime0.04
time0.158834934235
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory21712000
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, 0.048 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq
[main] Real time: 0.108 sec; CPU: 0.020 sec
systime0.028
time0.135224819183
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/E_coli.fasta reads.fastq -t 4 > out_bwamem.sam
memory150844000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 150000 sequences (15540421 bp)...
[M::mem_process_seqs] Processed 150000 reads in 32.952 CPU sec, 14.932 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads.fastq
[main] Real time: 24.847 sec; CPU: 33.648 sec
systime0.812
time24.9133081436
usrtime32.864
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558