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 Mapped14444396.295%
Wrongly Mapped55573.705%
Not Mapped00.0%
Total150000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position55573.705%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.981100
Precision0.963000
Recall1.000000
Timing
Raw Mapping Time2.460s
Effective Mapping Time2.445s
Effective Init Time0.015s
Effective Time MeasureWall clock
Mapping Time (Wall)2.460s
Mapping Time (CPU)6.723s
Mapping Time (CPU User)6.625s
Mapping Time (CPU System)0.098s
Init Time (Wall)0.015s
Init Time (CPU)0.011s
Init Time (CPU User)0.000s
Init Time (CPU System)0.011s
Additional Information
Mapper Memory Usage139 MB
Total Test Runtime (Wall)10.302s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory19292000
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: /project2/NextGenMapTest/Teaser/software/bwa mem -t 4 /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq

[main] Real time: 0.011 sec; CPU: 0.008 sec
systime0.011998
time0.0195059776306
usrtime0.0
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory19292000
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: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa mem -t 4 /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq

[main] Real time: 0.009 sec; CPU: 0.008 sec
systime0.010998
time0.014888048172
usrtime0.0
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads.fastq -t 4 > out_bwamem.sam
memory139588000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 150000 sequences (15000000 bp)...

[M::mem_process_seqs] Processed 150000 reads in 6.582 CPU sec, 1.654 real sec

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa mem -t 4 /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads.fastq

[main] Real time: 2.450 sec; CPU: 6.716 sec
systime0.097985
time2.45971393585
usrtime6.624992
working_directory/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test