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 Mapped6930.116%
Wrongly Mapped55431292.562%
Not Mapped438537.323%
Total598858100.0%
Read Failure Statistics
Not mapped438537.323%
Missing in mapper output00.0%
Mapped to wrong chromosome45599076.143%
Mapped to wrong position9832216.418%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment46
Secondary Alignments0
F-Measure0.002300
Precision0.001200
Recall0.015600
Timing
Raw Mapping Time192.609s
Effective Mapping Time192.464s
Effective Init Time0.145s
Effective Time MeasureCPU
Mapping Time (Wall)59.178s
Mapping Time (CPU)192.609s
Mapping Time (CPU User)191.091s
Mapping Time (CPU System)1.518s
Init Time (Wall)0.179s
Init Time (CPU)0.145s
Init Time (CPU User)0.007s
Init Time (CPU System)0.138s
Additional Information
Mapper Memory Usage634 MB
Total Test Runtime (Wall)95.189s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory247280000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.176 sec; CPU: 0.143 sec
systime0.141978
time0.181478977203
usrtime0.006998
working_directory/project/teaser/genometeaser/tests_generated/3d3edd8a6a451905ff28f5063d73cc4e

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory247284000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.173 sec; CPU: 0.140 sec
systime0.137979
time0.178572177887
usrtime0.006998
working_directory/project/teaser/genometeaser/tests_generated/3d3edd8a6a451905ff28f5063d73cc4e

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq -t 4 > out_bwasw.sam
memory634748000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 598858 sequences/pairs (35931480 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 59.167 sec; CPU: 192.597 sec
systime1.517769
time59.177793026
usrtime191.090949
working_directory/project/teaser/genometeaser/tests_generated/3d3edd8a6a451905ff28f5063d73cc4e