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 Mapped68523084.974%
Wrongly Mapped9273811.5%
Not Mapped284363.526%
Total806404100.0%
Read Failure Statistics
Not mapped284363.526%
Missing in mapper output00.0%
Mapped to wrong chromosome561306.961%
Mapped to wrong position366084.54%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment70
Secondary Alignments0
F-Measure0.918800
Precision0.880800
Recall0.960200
Timing
Raw Mapping Time1167.052s
Effective Mapping Time904.968s
Effective Init Time262.084s
Effective Time MeasureCPU
Mapping Time (Wall)512.221s
Mapping Time (CPU)1167.052s
Mapping Time (CPU User)821.880s
Mapping Time (CPU System)345.172s
Init Time (Wall)266.751s
Init Time (CPU)262.084s
Init Time (CPU User)0.120s
Init Time (CPU System)261.964s
Additional Information
Mapper Memory Usage8758 MB
Total Test Runtime (Wall)1156.621s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.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/M_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory8272240000
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/M_musculus.fasta reads_base.fastq
[main] Real time: 269.609 sec; CPU: 265.164 sec
systime265.064
time269.733865023
usrtime0.116
working_directory/project/teaser/genometeaser/tests_generated/a720be7d510db33409606fe9fee515f7

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory8272240000
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/M_musculus.fasta reads_base.fastq
[main] Real time: 266.717 sec; CPU: 262.064 sec
systime261.964
time266.750804186
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/a720be7d510db33409606fe9fee515f7

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwasw.sam
memory8758620000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 666668 sequences/pairs (40000080 bp) ...
[bsw2_aln] read 139736 sequences/pairs (8384160 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq
[main] Real time: 512.128 sec; CPU: 1166.988 sec
systime345.172
time512.22147584
usrtime821.88
working_directory/project/teaser/genometeaser/tests_generated/a720be7d510db33409606fe9fee515f7