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 Mapped52926988.38%
Wrongly Mapped6949611.605%
Not Mapped930.016%
Total598858100.0%
Read Failure Statistics
Not mapped930.016%
Missing in mapper output00.0%
Mapped to wrong chromosome411386.869%
Mapped to wrong position283584.735%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments1
F-Measure0.938300
Precision0.883900
Recall0.999800
Timing
Raw Mapping Time82.068s
Effective Mapping Time81.832s
Effective Init Time0.236s
Effective Time MeasureCPU
Mapping Time (Wall)32.091s
Mapping Time (CPU)82.068s
Mapping Time (CPU User)79.032s
Mapping Time (CPU System)3.036s
Init Time (Wall)0.304s
Init Time (CPU)0.236s
Init Time (CPU User)0.020s
Init Time (CPU System)0.216s
Additional Information
Mapper Memory Usage892 MB
Total Test Runtime (Wall)101.848s
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
memory250616000
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: 0.278 sec; CPU: 0.228 sec
systime0.236
time0.316954851151
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/4f9da0407e9bae0f2cd779a07f7552b0

/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 0.008 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: 0.273 sec; CPU: 0.224 sec
systime0.216
time0.304149866104
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/4f9da0407e9bae0f2cd779a07f7552b0

/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
memory892220000
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 80.488 CPU sec, 20.327 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: 32.015 sec; CPU: 82.048 sec
systime3.036
time32.0910210609
usrtime79.032
working_directory/project/teaser/genometeaser/tests_generated/4f9da0407e9bae0f2cd779a07f7552b0