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 Mapped29523098.684%
Wrongly Mapped39381.316%
Not Mapped00.0%
Total299168100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome10630.355%
Mapped to wrong position28750.961%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.993400
Precision0.986800
Recall1.000000
Timing
Raw Mapping Time44.588s
Effective Mapping Time44.388s
Effective Init Time0.200s
Effective Time MeasureCPU
Mapping Time (Wall)19.695s
Mapping Time (CPU)44.588s
Mapping Time (CPU User)43.376s
Mapping Time (CPU System)1.212s
Init Time (Wall)0.251s
Init Time (CPU)0.200s
Init Time (CPU User)0.012s
Init Time (CPU System)0.188s
Additional Information
Mapper Memory Usage433 MB
Total Test Runtime (Wall)61.907s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam
memory209228000
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 0.004 CPU sec, 0.002 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.214 sec; CPU: 0.192 sec
systime0.2
time0.235747098923
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwamem.sam
memory209224000
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 0.004 CPU sec, 0.002 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.221 sec; CPU: 0.192 sec
systime0.188
time0.251386880875
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300

/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory433600000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 299168 sequences (29916800 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 131666, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (376, 399, 421)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (286, 511)
[M::mem_pestat] mean and std.dev: (398.62, 32.86)
[M::mem_pestat] low and high boundaries for proper pairs: (241, 556)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 299168 reads in 43.680 CPU sec, 11.007 real sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq reads2.fastq
[main] Real time: 19.649 sec; CPU: 44.528 sec
systime1.212
time19.6954009533
usrtime43.376
working_directory/project/teaser/genometeaser/tests_generated/337f8b971fac4ff7ee4490260598b300