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 Mapped12023949.702%
Wrongly Mapped2544210.517%
Not Mapped9624039.782%
Total241921100.0%
Read Failure Statistics
Not mapped9445639.044%
Missing in mapper output17840.737%
Mapped to wrong chromosome161266.666%
Mapped to wrong position93163.851%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment3376
Secondary Alignments0
F-Measure0.667300
Precision0.825400
Recall0.560000
Timing
Raw Mapping Time91.019s
Effective Mapping Time40.096s
Effective Init Time50.923s
Effective Time MeasureWall clock
Mapping Time (Wall)91.019s
Mapping Time (CPU)173.587s
Mapping Time (CPU User)164.981s
Mapping Time (CPU System)8.606s
Init Time (Wall)50.923s
Init Time (CPU)9.063s
Init Time (CPU User)0.053s
Init Time (CPU System)9.010s
Additional Information
Mapper Memory Usage8610 MB
Total Test Runtime (Wall)211.273s
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: 59.827 sec; CPU: 9.380 sec
systime9.327581
time59.8824300766
usrtime0.054991
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M3_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
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: 50.905 sec; CPU: 9.059 sec
systime9.00963
time50.9226298332
usrtime0.052991
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M3_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
memory8610320000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[bsw2_aln] read 186542 sequences/pairs (40000225 bp) ...

[bsw2_aln] read 55379 sequences/pairs (11874128 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: 90.952 sec; CPU: 173.579 sec
systime8.605691
time91.0190529823
usrtime164.980919
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M3_n