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 Mapped21831090.24%
Wrongly Mapped225979.341%
Not Mapped10140.419%
Total241921100.0%
Read Failure Statistics
Not mapped10140.419%
Missing in mapper output00.0%
Mapped to wrong chromosome94803.919%
Mapped to wrong position131175.422%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments851
F-Measure0.948700
Precision0.906200
Recall0.995400
Timing
Raw Mapping Time154.668s
Effective Mapping Time109.973s
Effective Init Time44.695s
Effective Time MeasureWall clock
Mapping Time (Wall)154.668s
Mapping Time (CPU)471.833s
Mapping Time (CPU User)465.350s
Mapping Time (CPU System)6.483s
Init Time (Wall)44.695s
Init Time (CPU)8.562s
Init Time (CPU User)0.038s
Init Time (CPU System)8.524s
Additional Information
Mapper Memory Usage9086 MB
Total Test Runtime (Wall)271.027s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

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

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory8267892000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 1 sequences (60 bp)...

[M::mem_process_seqs] Processed 1 reads in 0.002 CPU sec, 0.034 real sec

[main] Version: 0.7.12-r1039

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

[main] Real time: 60.696 sec; CPU: 10.716 sec
systime10.676376
time60.7220628262
usrtime0.042993
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M3_n

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

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory8264980000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 1 sequences (60 bp)...

[M::mem_process_seqs] Processed 1 reads in 0.002 CPU sec, 0.003 real sec

[main] Version: 0.7.12-r1039

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

[main] Real time: 44.633 sec; CPU: 8.559 sec
systime8.523704
time44.6946310997
usrtime0.037994
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M3_n

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

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads.fastq -t 4 > out_bwamem.sam
memory9086480000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 186542 sequences (40000225 bp)...

[M::process] read 55379 sequences (11874128 bp)...

[M::mem_process_seqs] Processed 186542 reads in 360.448 CPU sec, 90.675 real sec

[M::mem_process_seqs] Processed 55379 reads in 105.112 CPU sec, 26.424 real sec

[main] Version: 0.7.12-r1039

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

[main] Real time: 154.631 sec; CPU: 471.816 sec
systime6.483014
time154.667797804
usrtime465.350256
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M3_n