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 Mapped2199284100.0%
Total2199284100.0%
Read Failure Statistics
Not mapped2199284100.0%
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 Time11.824s
Effective Mapping Time0.116s
Effective Init Time11.707s
Effective Time MeasureWall clock
Mapping Time (Wall)11.824s
Mapping Time (CPU)6.505s
Mapping Time (CPU User)4.055s
Mapping Time (CPU System)2.450s
Init Time (Wall)11.707s
Init Time (CPU)2.307s
Init Time (CPU User)0.040s
Init Time (CPU System)2.267s
Additional Information
Mapper Memory Usage8992 MB
Total Test Runtime (Wall)159.625s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/m_musculus.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/m_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory8270600000
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/m_musculus.fasta reads_base.fastq

[main] Real time: 89.866 sec; CPU: 4.212 sec
systime4.172365
time89.9333250523
usrtime0.042993
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M4_n

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

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory8253260000
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/m_musculus.fasta reads_base.fastq

[main] Real time: 11.591 sec; CPU: 2.303 sec
systime2.266655
time11.7073860168
usrtime0.039993
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M4_n

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

command/project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads.fastq -t 4 > out_bwasw.sam
memory8992232000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[bsw2_aln] read 1818182 sequences/pairs (40000004 bp) ...

[bsw2_aln] read 381102 sequences/pairs (8384244 bp) ...

[main] Version: 0.7.12-r1039

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

[main] Real time: 11.700 sec; CPU: 6.496 sec
systime2.449627
time11.8236701488
usrtime4.055383
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M4_n