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 Mapped14752898.352%
Wrongly Mapped24721.648%
Not Mapped00.0%
Total150000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome20311.354%
Mapped to wrong position4410.294%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.991700
Precision0.983500
Recall1.000000
Timing
Raw Mapping Time12.410s
Effective Mapping Time12.379s
Effective Init Time0.031s
Effective Time MeasureCPU
Mapping Time (Wall)3.761s
Mapping Time (CPU)12.410s
Mapping Time (CPU User)12.223s
Mapping Time (CPU System)0.187s
Init Time (Wall)0.065s
Init Time (CPU)0.031s
Init Time (CPU User)0.005s
Init Time (CPU System)0.026s
Additional Information
Mapper Memory Usage149 MB
Total Test Runtime (Wall)12.245s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Cryptosporidium.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/Cryptosporidium.fasta reads_base.fastq -t 4 > out_bwamem.sam

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Cryptosporidium.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory33552000
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 0.001 CPU sec, 0.001 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Cryptosporidium.fasta reads_base.fastq
[main] Real time: 0.057 sec; CPU: 0.027 sec
systime0.028995
time0.0643239021301
usrtime0.001999
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Cryptosporidium.fasta reads_base.fastq -t 4 > out_bwamem.sam
memory33552000
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: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Cryptosporidium.fasta reads_base.fastq
[main] Real time: 0.058 sec; CPU: 0.027 sec
systime0.025996
time0.0650129318237
usrtime0.004999
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

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

command/project/teaser/genometeaser/software/bwa mem /project/teaser/genometeaser/references/Cryptosporidium.fasta reads1.fastq reads2.fastq -t 4 > out_bwamem.sam
memory149136000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 150000 sequences (15000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 71610, 78, 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: (77, 99, 121)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 209)
[M::mem_pestat] mean and std.dev: (99.05, 32.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 253)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (1, 1, 1)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1)
[M::mem_pestat] mean and std.dev: (1.00, 0.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 150000 reads in 12.212 CPU sec, 3.088 real sec
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa mem -t 4 /project/teaser/genometeaser/references/Cryptosporidium.fasta reads1.fastq reads2.fastq
[main] Real time: 3.751 sec; CPU: 12.402 sec
systime0.186971
time3.76119804382
usrtime12.223141
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae