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 Mapped54563091.112%
Wrongly Mapped532288.888%
Not Mapped00.0%
Total598858100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome284704.754%
Mapped to wrong position247584.134%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.953500
Precision0.911100
Recall1.000000
Timing
Raw Mapping Time130.220s
Effective Mapping Time127.656s
Effective Init Time2.564s
Effective Time MeasureCPU
Mapping Time (Wall)46.972s
Mapping Time (CPU)130.220s
Mapping Time (CPU User)121.852s
Mapping Time (CPU System)8.368s
Init Time (Wall)2.661s
Init Time (CPU)2.564s
Init Time (CPU User)0.008s
Init Time (CPU System)2.556s
Additional Information
Mapper Memory Usage858 MB
Total Test Runtime (Wall)102.720s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta 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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory248856000
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 0.044 CPU sec, 0.047 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 4.481 sec; CPU: 4.340 sec
systime4.328
time4.50412201881
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory248848000
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 0.020 CPU sec, 0.019 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq
[main] Real time: 2.632 sec; CPU: 2.556 sec
systime2.556
time2.6611790657
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory858412000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 598858 sequences (35931480 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 246109, 1, 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: (126, 148, 171)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (36, 261)
[M::mem_pestat] mean and std.dev: (148.40, 32.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 306)
[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 598858 reads in 126.336 CPU sec, 32.343 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq reads2.fastq
[main] Real time: 46.914 sec; CPU: 130.180 sec
systime8.368
time46.9715080261
usrtime121.852
working_directory/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62