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 Mapped51480085.964%
Wrongly Mapped6859611.454%
Not Mapped154622.582%
Total598858100.0%
Read Failure Statistics
Not mapped154622.582%
Missing in mapper output00.0%
Mapped to wrong chromosome423687.075%
Mapped to wrong position262284.38%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment22
Secondary Alignments0
F-Measure0.924500
Precision0.882400
Recall0.970800
Timing
Raw Mapping Time197.276s
Effective Mapping Time197.028s
Effective Init Time0.248s
Effective Time MeasureCPU
Mapping Time (Wall)64.028s
Mapping Time (CPU)197.276s
Mapping Time (CPU User)188.732s
Mapping Time (CPU System)8.544s
Init Time (Wall)0.294s
Init Time (CPU)0.248s
Init Time (CPU User)0.024s
Init Time (CPU System)0.224s
Additional Information
Mapper Memory Usage686 MB
Total Test Runtime (Wall)135.022s
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
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: 0.305 sec; CPU: 0.232 sec
systime0.232
time0.327642917633
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/940d34bf07c6143b2e6e8116a29b2b51

/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
memory250356000
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: 0.267 sec; CPU: 0.232 sec
systime0.224
time0.293583869934
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/940d34bf07c6143b2e6e8116a29b2b51

/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
memory686256000
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: 63.990 sec; CPU: 197.240 sec
systime8.544
time64.0279891491
usrtime188.732
working_directory/project/teaser/genometeaser/tests_generated/940d34bf07c6143b2e6e8116a29b2b51