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 Mapped52902388.339%
Wrongly Mapped6974811.647%
Not Mapped870.015%
Total598858100.0%
Read Failure Statistics
Not mapped870.015%
Missing in mapper output00.0%
Mapped to wrong chromosome415376.936%
Mapped to wrong position282114.711%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.938100
Precision0.883500
Recall0.999800
Timing
Raw Mapping Time85.588s
Effective Mapping Time85.288s
Effective Init Time0.300s
Effective Time MeasureCPU
Mapping Time (Wall)39.457s
Mapping Time (CPU)85.588s
Mapping Time (CPU User)81.708s
Mapping Time (CPU System)3.880s
Init Time (Wall)4.287s
Init Time (CPU)0.300s
Init Time (CPU User)0.020s
Init Time (CPU System)0.280s
Additional Information
Mapper Memory Usage894 MB
Total Test Runtime (Wall)142.514s
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, 0.003 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: 6.059 sec; CPU: 0.228 sec
systime0.216
time7.47591495514
usrtime0.028
working_directory/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0

/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
memory248784000
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: 3.086 sec; CPU: 0.288 sec
systime0.28
time4.28682088852
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0

/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
memory894852000
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 83.988 CPU sec, 21.348 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: 38.398 sec; CPU: 85.572 sec
systime3.88
time39.4574928284
usrtime81.708
working_directory/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0