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 Mapped51468385.944%
Wrongly Mapped6877511.484%
Not Mapped154002.572%
Total598858100.0%
Read Failure Statistics
Not mapped154002.572%
Missing in mapper output00.0%
Mapped to wrong chromosome426867.128%
Mapped to wrong position260894.356%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment24
Secondary Alignments0
F-Measure0.924400
Precision0.882100
Recall0.970900
Timing
Raw Mapping Time295.204s
Effective Mapping Time279.652s
Effective Init Time15.552s
Effective Time MeasureCPU
Mapping Time (Wall)114.517s
Mapping Time (CPU)295.204s
Mapping Time (CPU User)262.936s
Mapping Time (CPU System)32.268s
Init Time (Wall)15.937s
Init Time (CPU)15.552s
Init Time (CPU User)0.012s
Init Time (CPU System)15.540s
Additional Information
Mapper Memory Usage684 MB
Total Test Runtime (Wall)231.603s
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
memory248996000
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: 15.285 sec; CPU: 14.836 sec
systime14.844
time15.3394570351
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b

/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
memory248996000
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: 15.906 sec; CPU: 15.540 sec
systime15.54
time15.9371860027
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b

/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
memory684884000
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: 114.445 sec; CPU: 295.148 sec
systime32.268
time114.517436981
usrtime262.936
working_directory/project/teaser/genometeaser/tests_generated/f2a6f25cabc55338e734f1adbe44516b