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 Mapped80653780.807%
Wrongly Mapped12674012.698%
Not Mapped648206.494%
Total998097100.0%
Read Failure Statistics
Not mapped648206.494%
Missing in mapper output00.0%
Mapped to wrong chromosome804768.063%
Mapped to wrong position462634.635%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.893900
Precision0.864200
Recall0.925600
Timing
Raw Mapping Time117.984s
Effective Mapping Time114.708s
Effective Init Time3.276s
Effective Time MeasureCPU
Mapping Time (Wall)57.227s
Mapping Time (CPU)117.984s
Mapping Time (CPU User)106.688s
Mapping Time (CPU System)11.296s
Init Time (Wall)7.255s
Init Time (CPU)3.276s
Init Time (CPU User)0.024s
Init Time (CPU System)3.252s
Additional Information
Mapper Memory Usage1392 MB
Total Test Runtime (Wall)208.340s
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
memory313608000
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: 4.223 sec; CPU: 3.904 sec
systime3.924
time4.2454688549
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c

/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
memory313608000
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: 6.602 sec; CPU: 3.248 sec
systime3.252
time7.25456309319
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c

/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
memory1392808000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 998097 sequences (35931492 bp)...
[M::mem_process_seqs] Processed 998097 reads in 112.652 CPU sec, 29.056 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: 55.128 sec; CPU: 117.924 sec
systime11.296
time57.2271809578
usrtime106.688
working_directory/project/teaser/genometeaser/tests_generated/47ed064b8a7255de5257058de7620d9c