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 Mapped50025795.677%
Wrongly Mapped205023.921%
Not Mapped21010.402%
Total522860100.0%
Read Failure Statistics
Not mapped21010.402%
Missing in mapper output00.0%
Mapped to wrong chromosome139402.666%
Mapped to wrong position65621.255%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.977900
Precision0.960600
Recall0.995800
Timing
Raw Mapping Time260.464s
Effective Mapping Time250.832s
Effective Init Time9.632s
Effective Time MeasureCPU
Mapping Time (Wall)127.791s
Mapping Time (CPU)260.464s
Mapping Time (CPU User)245.744s
Mapping Time (CPU System)14.720s
Init Time (Wall)9.826s
Init Time (CPU)9.632s
Init Time (CPU User)0.208s
Init Time (CPU System)9.424s
Additional Information
Mapper Memory Usage4892 MB
Total Test Runtime (Wall)675.602s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory4599032000
return0
status1
stderr
None
stdout
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 266.838 sec; CPU: 5.720 sec
[bwa_aln_core] convert to sequence coordinate... 6.51 sec
[bwa_aln_core] refine gapped alignments... 1.31 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 204.297 sec; CPU: 7.828 sec
systime13.36
time471.197770834
usrtime0.2
working_directory/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory4599020000
return0
status1
stderr
None
stdout
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 3.057 sec; CPU: 3.024 sec
[bwa_aln_core] convert to sequence coordinate... 5.58 sec
[bwa_aln_core] refine gapped alignments... 1.01 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 6.702 sec; CPU: 6.600 sec
systime9.424
time9.82629680634
usrtime0.208
working_directory/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/H_sapiens.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
memory4892304000
return0
status1
stderr
None
stdout
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 102.29 sec
[bwa_aln_core] write to the disk... 0.12 sec
[bwa_aln_core] 261430 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq
[main] Real time: 32.863 sec; CPU: 106.044 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 100.24 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 261430 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads2.fastq
[main] Real time: 33.726 sec; CPU: 104.656 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (80, 100, 121)
[infer_isize] low and high boundaries: 60 and 203 for estimating avg and std
[infer_isize] inferred external isize from 224666 pairs: 102.614 +/- 27.670
[infer_isize] skewness: 0.554; kurtosis: -0.241; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 298 (7.05 sigma)
[bwa_sai2sam_pe_core] time elapses: 43.73 sec
[bwa_sai2sam_pe_core] changing coordinates of 7959 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 3249 out of 4615 Q17 singletons are mated.
[bwa_paired_sw] 563 out of 28796 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.33 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.96 sec
[bwa_sai2sam_pe_core] print alignments... 1.45 sec
[bwa_sai2sam_pe_core] 261430 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/H_sapiens.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq
[main] Real time: 61.070 sec; CPU: 49.704 sec
systime14.72
time127.790576935
usrtime245.744
working_directory/project/teaser/genometeaser/tests_generated/24d206dec9772782e6efab15944abfc6