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 Mapped00.0%
Wrongly Mapped00.0%
Not Mapped1633249100.0%
Total1633249100.0%
Read Failure Statistics
Not mapped1633249100.0%
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 alignment0
Secondary Alignments0
F-Measure0.000000
Precision0.000000
Recall0.000000
Timing
Raw Mapping Time3.585s
Effective Mapping Time3.482s
Effective Init Time0.104s
Effective Time MeasureWall clock
Mapping Time (Wall)3.585s
Mapping Time (CPU)3.412s
Mapping Time (CPU User)3.016s
Mapping Time (CPU System)0.397s
Init Time (Wall)0.104s
Init Time (CPU)0.059s
Init Time (CPU User)0.004s
Init Time (CPU System)0.055s
Additional Information
Mapper Memory Usage897 MB
Total Test Runtime (Wall)39.359s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory247436000
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: /project2/NextGenMapTest/Teaser/software/bwa bwasw -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq

[main] Real time: 0.061 sec; CPU: 0.056 sec
systime0.052991
time0.0680248737335
usrtime0.005999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D4_n

/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory247500000
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: /project2/NextGenMapTest/Teaser/software/bwa bwasw -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq

[main] Real time: 0.061 sec; CPU: 0.056 sec
systime0.054991
time0.103645086288
usrtime0.003999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D4_n

/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwasw.sam

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwasw.sam
memory897744000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[bsw2_aln] read 1633249 sequences/pairs (35931478 bp) ...

[main] Version: 0.7.12-r1039

[main] CMD: /project2/NextGenMapTest/Teaser/software/bwa bwasw -t 4 /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq

[main] Real time: 3.575 sec; CPU: 3.404 sec
systime0.396939
time3.58543086052
usrtime3.015541
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D4_n