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 Mapped32411390.203%
Wrongly Mapped352019.797%
Not Mapped00.0%
Total359314100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome195945.453%
Mapped to wrong position156074.344%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.948500
Precision0.902000
Recall1.000000
Timing
Raw Mapping Time67.700s
Effective Mapping Time67.424s
Effective Init Time0.276s
Effective Time MeasureCPU
Mapping Time (Wall)26.537s
Mapping Time (CPU)67.700s
Mapping Time (CPU User)66.248s
Mapping Time (CPU System)1.452s
Init Time (Wall)0.326s
Init Time (CPU)0.276s
Init Time (CPU User)0.016s
Init Time (CPU System)0.260s
Additional Information
Mapper Memory Usage606 MB
Total Test Runtime (Wall)64.616s
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
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 0.000 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: 0.278 sec; CPU: 0.244 sec
systime0.232
time0.297417879105
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c

/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
memory252404000
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, 0.003 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: 0.293 sec; CPU: 0.260 sec
systime0.26
time0.326078891754
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c

/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
memory606156000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 359314 sequences (35931400 bp)...
[M::mem_process_seqs] Processed 359314 reads in 66.632 CPU sec, 16.742 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: 26.484 sec; CPU: 67.688 sec
systime1.452
time26.5372149944
usrtime66.248
working_directory/project/teaser/genometeaser/tests_generated/0099470d1042c35fd42f63c3beb9132c