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 Mapped10.001%
Wrongly Mapped00.0%
Not Mapped14999299.999%
Total149993100.0%
Read Failure Statistics
Not mapped14999299.999%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position00.0%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment7
Secondary Alignments0
F-Measure0.000000
Precision1.000000
Recall0.000000
Timing
Raw Mapping Time77.716s
Effective Mapping Time77.660s
Effective Init Time0.056s
Effective Time MeasureCPU
Mapping Time (Wall)33.553s
Mapping Time (CPU)77.716s
Mapping Time (CPU User)75.704s
Mapping Time (CPU System)2.012s
Init Time (Wall)0.078s
Init Time (CPU)0.056s
Init Time (CPU User)0.008s
Init Time (CPU System)0.048s
Additional Information
Mapper Memory Usage190 MB
Total Test Runtime (Wall)63.755s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.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/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory21068000
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/E_coli.fasta reads_base.fastq
[main] Real time: 0.109 sec; CPU: 0.044 sec
systime0.044
time0.136445045471
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory21068000
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/E_coli.fasta reads_base.fastq
[main] Real time: 0.063 sec; CPU: 0.044 sec
systime0.048
time0.0780141353607
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/E_coli.fasta reads.fastq -t 4 > out_bwasw.sam
memory190116000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 150000 sequences/pairs (25877072 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads.fastq
[main] Real time: 33.479 sec; CPU: 77.676 sec
systime2.012
time33.5534541607
usrtime75.704
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923