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 Mapped24028696.114%
Wrongly Mapped96553.862%
Not Mapped590.024%
Total250000100.0%
Read Failure Statistics
Not mapped590.024%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position96553.862%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.980200
Precision0.961400
Recall0.999800
Timing
Raw Mapping Time11.200s
Effective Mapping Time11.168s
Effective Init Time0.032s
Effective Time MeasureCPU
Mapping Time (Wall)8.143s
Mapping Time (CPU)11.200s
Mapping Time (CPU User)10.376s
Mapping Time (CPU System)0.824s
Init Time (Wall)0.091s
Init Time (CPU)0.032s
Init Time (CPU User)0.012s
Init Time (CPU System)0.020s
Additional Information
Mapper Memory Usage146 MB
Total Test Runtime (Wall)39.755s
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
memory25616000
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, 0.003 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: 0.053 sec; CPU: 0.024 sec
systime0.024
time0.0741081237793
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f

/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
memory25616000
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, 0.001 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: 0.058 sec; CPU: 0.024 sec
systime0.02
time0.0908269882202
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f

/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
memory146420000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 250000 sequences (15000000 bp)...
[M::mem_process_seqs] Processed 250000 reads in 10.556 CPU sec, 2.696 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: 8.106 sec; CPU: 11.176 sec
systime0.824
time8.14254212379
usrtime10.376
working_directory/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f