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 Mapped3240897.225%
Wrongly Mapped9252.775%
Not Mapped00.0%
Total33333100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position9252.775%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.985900
Precision0.972200
Recall1.000000
Timing
Raw Mapping Time50.220s
Effective Mapping Time50.188s
Effective Init Time0.032s
Effective Time MeasureCPU
Mapping Time (Wall)16.149s
Mapping Time (CPU)50.220s
Mapping Time (CPU User)49.664s
Mapping Time (CPU System)0.556s
Init Time (Wall)0.074s
Init Time (CPU)0.032s
Init Time (CPU User)0.004s
Init Time (CPU System)0.028s
Additional Information
Mapper Memory Usage113 MB
Total Test Runtime (Wall)33.533s
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
memory14188000
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, 0.002 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: 0.050 sec; CPU: 0.024 sec
systime0.032
time0.0778949260712
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e

/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
memory14188000
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 0.000 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: 0.049 sec; CPU: 0.024 sec
systime0.028
time0.0738489627838
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e

/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
memory113664000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 33333 sequences (14999850 bp)...
[M::mem_process_seqs] Processed 33333 reads in 49.680 CPU sec, 12.423 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: 16.115 sec; CPU: 50.212 sec
systime0.556
time16.1485979557
usrtime49.664
working_directory/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e