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 Mapped51427885.876%
Wrongly Mapped6914811.547%
Not Mapped154322.577%
Total598858100.0%
Read Failure Statistics
Not mapped154322.577%
Missing in mapper output00.0%
Mapped to wrong chromosome429777.176%
Mapped to wrong position261714.37%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment20
Secondary Alignments0
F-Measure0.924000
Precision0.881500
Recall0.970900
Timing
Raw Mapping Time215.460s
Effective Mapping Time215.164s
Effective Init Time0.296s
Effective Time MeasureCPU
Mapping Time (Wall)94.051s
Mapping Time (CPU)215.460s
Mapping Time (CPU User)205.888s
Mapping Time (CPU System)9.572s
Init Time (Wall)6.508s
Init Time (CPU)0.296s
Init Time (CPU User)0.020s
Init Time (CPU System)0.276s
Additional Information
Mapper Memory Usage685 MB
Total Test Runtime (Wall)166.616s
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
memory248780000
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: 6.237 sec; CPU: 0.224 sec
systime0.236
time7.65360999107
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0

/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
memory250352000
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: 5.173 sec; CPU: 0.284 sec
systime0.276
time6.50803399086
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0

/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
memory685792000
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: 92.813 sec; CPU: 215.420 sec
systime9.572
time94.0509750843
usrtime205.888
working_directory/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0