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 Mapped53028688.55%
Wrongly Mapped6847011.433%
Not Mapped1020.017%
Total598858100.0%
Read Failure Statistics
Not mapped1020.017%
Missing in mapper output00.0%
Mapped to wrong chromosome405806.776%
Mapped to wrong position278904.657%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.939300
Precision0.885600
Recall0.999800
Timing
Raw Mapping Time86.152s
Effective Mapping Time85.912s
Effective Init Time0.240s
Effective Time MeasureCPU
Mapping Time (Wall)33.065s
Mapping Time (CPU)86.152s
Mapping Time (CPU User)82.488s
Mapping Time (CPU System)3.664s
Init Time (Wall)0.326s
Init Time (CPU)0.240s
Init Time (CPU User)0.008s
Init Time (CPU System)0.232s
Additional Information
Mapper Memory Usage896 MB
Total Test Runtime (Wall)103.546s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory248788000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.283 sec; CPU: 0.224 sec
systime0.22
time0.316092014313
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/9df2b6f30934a6f088552bf04d77f27b

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory250352000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.283 sec; CPU: 0.224 sec
systime0.232
time0.325721025467
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/9df2b6f30934a6f088552bf04d77f27b

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwamem.sam
memory896860000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 598858 sequences (35931480 bp)...
[M::mem_process_seqs] Processed 598858 reads in 84.844 CPU sec, 21.549 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 33.003 sec; CPU: 86.140 sec
systime3.664
time33.0648748875
usrtime82.488
working_directory/project/teaser/genometeaser/tests_generated/9df2b6f30934a6f088552bf04d77f27b