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 Mapped16151289.9%
Wrongly Mapped175229.753%
Not Mapped6230.347%
Total179657100.0%
Read Failure Statistics
Not mapped6230.347%
Missing in mapper output00.0%
Mapped to wrong chromosome74394.141%
Mapped to wrong position100835.612%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments166
F-Measure0.946800
Precision0.902100
Recall0.996200
Timing
Raw Mapping Time34.085s
Effective Mapping Time33.958s
Effective Init Time0.127s
Effective Time MeasureWall clock
Mapping Time (Wall)34.085s
Mapping Time (CPU)126.492s
Mapping Time (CPU User)126.170s
Mapping Time (CPU System)0.322s
Init Time (Wall)0.127s
Init Time (CPU)0.060s
Init Time (CPU User)0.003s
Init Time (CPU System)0.057s
Additional Information
Mapper Memory Usage549 MB
Total Test Runtime (Wall)43.899s
Mapper Command Line: 
/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/d_melanogaster.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/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory251060000
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 0.003 CPU sec, 0.002 real sec

[main] Version: 0.7.12-r1039

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

[main] Real time: 0.150 sec; CPU: 0.061 sec
systime0.056991
time0.156754970551
usrtime0.006998
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D3_n

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

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory247292000
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, 0.001 real sec

[main] Version: 0.7.12-r1039

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

[main] Real time: 0.121 sec; CPU: 0.057 sec
systime0.056991
time0.12664103508
usrtime0.002999
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D3_n

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

command/project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta reads.fastq -t 4 > out_bwamem.sam
memory549340000
return0
status1
stderr

None
stdout

[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 179657 sequences (38492672 bp)...

[M::mem_process_seqs] Processed 179657 reads in 126.128 CPU sec, 31.663 real sec

[main] Version: 0.7.12-r1039

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

[main] Real time: 34.075 sec; CPU: 126.485 sec
systime0.321951
time34.0847110748
usrtime126.169819
working_directory/project2/NextGenMapTest/Teaser/tests_generated/D3_n