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 Mapped30187093.585%
Wrongly Mapped206916.415%
Not Mapped00.0%
Total322561100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome94762.938%
Mapped to wrong position112153.477%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments4
F-Measure0.966900
Precision0.935900
Recall1.000000
Timing
Raw Mapping Time123.025s
Effective Mapping Time34.208s
Effective Init Time88.817s
Effective Time MeasureWall clock
Mapping Time (Wall)123.025s
Mapping Time (CPU)171.865s
Mapping Time (CPU User)156.989s
Mapping Time (CPU System)14.876s
Init Time (Wall)88.817s
Init Time (CPU)18.386s
Init Time (CPU User)0.053s
Init Time (CPU System)18.333s
Additional Information
Mapper Memory Usage8813 MB
Total Test Runtime (Wall)317.182s
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
memory8263152000
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, 0.031 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: 91.912 sec; CPU: 21.047 sec
systime21.012805
time91.9536640644
usrtime0.036994
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_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
memory8269652000
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, 0.010 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: 88.711 sec; CPU: 18.382 sec
systime18.333212
time88.8168411255
usrtime0.052991
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_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
memory8813016000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 266668 sequences (40000200 bp)...

[M::process] read 55893 sequences (8383950 bp)...

[M::mem_process_seqs] Processed 266668 reads in 130.506 CPU sec, 32.890 real sec

[M::mem_process_seqs] Processed 55893 reads in 26.431 CPU sec, 6.641 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: 122.781 sec; CPU: 171.846 sec
systime14.875738
time123.024772882
usrtime156.989134
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_n