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 Mapped52833088.223%
Wrongly Mapped7043511.762%
Not Mapped930.016%
Total598858100.0%
Read Failure Statistics
Not mapped930.016%
Missing in mapper output00.0%
Mapped to wrong chromosome421567.039%
Mapped to wrong position282794.722%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.937400
Precision0.882400
Recall0.999800
Timing
Raw Mapping Time94.312s
Effective Mapping Time94.004s
Effective Init Time0.308s
Effective Time MeasureCPU
Mapping Time (Wall)35.587s
Mapping Time (CPU)94.312s
Mapping Time (CPU User)90.732s
Mapping Time (CPU System)3.580s
Init Time (Wall)0.353s
Init Time (CPU)0.308s
Init Time (CPU User)0.024s
Init Time (CPU System)0.284s
Additional Information
Mapper Memory Usage902 MB
Total Test Runtime (Wall)81.962s
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
memory248848000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.307 sec; CPU: 0.260 sec
systime0.252
time0.325237989426
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8

/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
memory248852000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.322 sec; CPU: 0.288 sec
systime0.284
time0.35297203064
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8

/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
memory902980000
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 92.408 CPU sec, 23.473 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 35.534 sec; CPU: 94.268 sec
systime3.58
time35.5865409374
usrtime90.732
working_directory/project/teaser/genometeaser/tests_generated/572b02d835a09aa985fb40e23486baf8