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 Mapped26808483.111%
Wrongly Mapped3258410.102%
Not Mapped218936.787%
Total322561100.0%
Read Failure Statistics
Not mapped218936.787%
Missing in mapper output00.0%
Mapped to wrong chromosome202416.275%
Mapped to wrong position123433.827%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment765
Secondary Alignments0
F-Measure0.907800
Precision0.891600
Recall0.924500
Timing
Raw Mapping Time122.909s
Effective Mapping Time56.809s
Effective Init Time66.100s
Effective Time MeasureWall clock
Mapping Time (Wall)122.909s
Mapping Time (CPU)255.850s
Mapping Time (CPU User)243.527s
Mapping Time (CPU System)12.323s
Init Time (Wall)66.100s
Init Time (CPU)11.779s
Init Time (CPU User)0.041s
Init Time (CPU System)11.738s
Additional Information
Mapper Memory Usage8592 MB
Total Test Runtime (Wall)282.879s
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
memory8270660000
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: 72.324 sec; CPU: 11.600 sec
systime11.537246
time72.3324229717
usrtime0.066989
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_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
memory8270608000
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: 65.881 sec; CPU: 11.776 sec
systime11.738215
time66.1003592014
usrtime0.040993
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_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
memory8592800000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[bsw2_aln] read 266668 sequences/pairs (40000200 bp) ...

[bsw2_aln] read 55893 sequences/pairs (8383950 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: 122.888 sec; CPU: 255.842 sec
systime12.323126
time122.909267902
usrtime243.526978
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_n