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 Mapped30.002%
Wrongly Mapped20.001%
Not Mapped14998899.997%
Total149993100.0%
Read Failure Statistics
Not mapped14998899.997%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position20.001%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment7
Secondary Alignments0
F-Measure0.000000
Precision0.600000
Recall0.000000
Timing
Raw Mapping Time38.772s
Effective Mapping Time38.740s
Effective Init Time0.032s
Effective Time MeasureCPU
Mapping Time (Wall)20.605s
Mapping Time (CPU)38.772s
Mapping Time (CPU User)37.708s
Mapping Time (CPU System)1.064s
Init Time (Wall)0.123s
Init Time (CPU)0.032s
Init Time (CPU User)0.000s
Init Time (CPU System)0.032s
Additional Information
Mapper Memory Usage169 MB
Total Test Runtime (Wall)48.332s
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
memory21068000
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: 0.126 sec; CPU: 0.036 sec
systime0.028
time0.159026861191
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923

/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
memory21068000
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: 0.096 sec; CPU: 0.020 sec
systime0.032
time0.123476982117
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923

/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
memory169212000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 150000 sequences (25877072 bp)...
[M::mem_process_seqs] Processed 150000 reads in 37.508 CPU sec, 10.257 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: 20.565 sec; CPU: 38.748 sec
systime1.064
time20.6047489643
usrtime37.708
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923