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 Mapped51543386.069%
Wrongly Mapped6817811.385%
Not Mapped152472.546%
Total598858100.0%
Read Failure Statistics
Not mapped152472.546%
Missing in mapper output00.0%
Mapped to wrong chromosome426627.124%
Mapped to wrong position255164.261%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment28
Secondary Alignments0
F-Measure0.925100
Precision0.883200
Recall0.971300
Timing
Raw Mapping Time384.676s
Effective Mapping Time381.948s
Effective Init Time2.728s
Effective Time MeasureCPU
Mapping Time (Wall)141.757s
Mapping Time (CPU)384.676s
Mapping Time (CPU User)367.032s
Mapping Time (CPU System)17.644s
Init Time (Wall)2.854s
Init Time (CPU)2.728s
Init Time (CPU User)0.016s
Init Time (CPU System)2.712s
Additional Information
Mapper Memory Usage684 MB
Total Test Runtime (Wall)230.661s
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
memory248864000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 2.135 sec; CPU: 2.068 sec
systime2.068
time2.15794992447
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3

/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
memory248860000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 2.791 sec; CPU: 2.712 sec
systime2.712
time2.85354709625
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3

/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
memory684864000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads.fastq
[main] Real time: 141.660 sec; CPU: 384.620 sec
systime17.644
time141.756763935
usrtime367.032
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3