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 Mapped21931591.556%
Wrongly Mapped200428.367%
Not Mapped1860.078%
Total239543100.0%
Read Failure Statistics
Not mapped1860.078%
Missing in mapper output00.0%
Mapped to wrong chromosome107174.474%
Mapped to wrong position93253.893%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments6
F-Measure0.955900
Precision0.916300
Recall0.999200
Timing
Raw Mapping Time27.833s
Effective Mapping Time27.732s
Effective Init Time0.102s
Effective Time MeasureWall clock
Mapping Time (Wall)27.833s
Mapping Time (CPU)101.995s
Mapping Time (CPU User)101.708s
Mapping Time (CPU System)0.288s
Init Time (Wall)0.102s
Init Time (CPU)0.059s
Init Time (CPU User)0.007s
Init Time (CPU System)0.052s
Additional Information
Mapper Memory Usage525 MB
Total Test Runtime (Wall)44.958s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory251052000
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 0.003 CPU sec, 0.002 real sec

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa mem -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq

[main] Real time: 0.064 sec; CPU: 0.059 sec
systime0.057991
time0.0700528621674
usrtime0.003999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_n

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory247280000
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 0.002 CPU sec, 0.001 real sec

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa mem -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq

[main] Real time: 0.061 sec; CPU: 0.056 sec
systime0.051992
time0.1017370224
usrtime0.006998
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_n

/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwamem.sam
memory525536000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 239543 sequences (35931450 bp)...

[M::mem_process_seqs] Processed 239543 reads in 101.660 CPU sec, 25.546 real sec

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa mem -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq

[main] Real time: 27.825 sec; CPU: 101.989 sec
systime0.287956
time27.833258152
usrtime101.707538
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D2_n