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 Mapped53007688.514%
Wrongly Mapped6869111.47%
Not Mapped910.015%
Total598858100.0%
Read Failure Statistics
Not mapped910.015%
Missing in mapper output00.0%
Mapped to wrong chromosome408966.829%
Mapped to wrong position277954.641%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments1
F-Measure0.939100
Precision0.885300
Recall0.999800
Timing
Raw Mapping Time80.072s
Effective Mapping Time79.820s
Effective Init Time0.252s
Effective Time MeasureCPU
Mapping Time (Wall)31.314s
Mapping Time (CPU)80.072s
Mapping Time (CPU User)77.400s
Mapping Time (CPU System)2.672s
Init Time (Wall)0.335s
Init Time (CPU)0.252s
Init Time (CPU User)0.020s
Init Time (CPU System)0.232s
Additional Information
Mapper Memory Usage890 MB
Total Test Runtime (Wall)99.108s
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
memory250620000
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 0.008 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: 0.266 sec; CPU: 0.232 sec
systime0.244
time0.366708993912
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/63224990d2f5aeaa3b674d6cbc4acc8f

/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: 0.270 sec; CPU: 0.232 sec
systime0.232
time0.335210084915
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/63224990d2f5aeaa3b674d6cbc4acc8f

/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
memory890004000
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 78.860 CPU sec, 19.976 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: 31.261 sec; CPU: 80.024 sec
systime2.672
time31.3140070438
usrtime77.4
working_directory/project/teaser/genometeaser/tests_generated/63224990d2f5aeaa3b674d6cbc4acc8f