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 Mapped51487285.976%
Wrongly Mapped6879711.488%
Not Mapped151892.536%
Total598858100.0%
Read Failure Statistics
Not mapped151892.536%
Missing in mapper output00.0%
Mapped to wrong chromosome427597.14%
Mapped to wrong position260384.348%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment35
Secondary Alignments0
F-Measure0.924600
Precision0.882100
Recall0.971300
Timing
Raw Mapping Time170.164s
Effective Mapping Time169.924s
Effective Init Time0.240s
Effective Time MeasureCPU
Mapping Time (Wall)55.096s
Mapping Time (CPU)170.164s
Mapping Time (CPU User)162.364s
Mapping Time (CPU System)7.800s
Init Time (Wall)0.297s
Init Time (CPU)0.240s
Init Time (CPU User)0.012s
Init Time (CPU System)0.228s
Additional Information
Mapper Memory Usage685 MB
Total Test Runtime (Wall)125.748s
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
memory248776000
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: 0.277 sec; CPU: 0.224 sec
systime0.232
time0.318894147873
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/4f9da0407e9bae0f2cd779a07f7552b0

/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
memory248900000
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: 0.271 sec; CPU: 0.224 sec
systime0.228
time0.296566009521
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/4f9da0407e9bae0f2cd779a07f7552b0

/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
memory685456000
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: 55.038 sec; CPU: 170.112 sec
systime7.8
time55.0960850716
usrtime162.364
working_directory/project/teaser/genometeaser/tests_generated/4f9da0407e9bae0f2cd779a07f7552b0