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 Mapped32037689.163%
Wrongly Mapped335489.337%
Not Mapped53901.5%
Total359314100.0%
Read Failure Statistics
Not mapped53901.5%
Missing in mapper output00.0%
Mapped to wrong chromosome179945.008%
Mapped to wrong position155544.329%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.942700
Precision0.905200
Recall0.983500
Timing
Raw Mapping Time84.673s
Effective Mapping Time84.414s
Effective Init Time0.259s
Effective Time MeasureCPU
Mapping Time (Wall)46.467s
Mapping Time (CPU)84.673s
Mapping Time (CPU User)83.950s
Mapping Time (CPU System)0.723s
Init Time (Wall)0.352s
Init Time (CPU)0.259s
Init Time (CPU User)0.013s
Init Time (CPU System)0.246s
Additional Information
Mapper Memory Usage445 MB
Total Test Runtime (Wall)64.840s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/D_melanogaster.fasta 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/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory212608000
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... 0.01 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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.145 sec; CPU: 0.113 sec
[bwa_aln_core] convert to sequence coordinate... 0.16 sec
[bwa_aln_core] refine gapped alignments... 0.03 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/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.236 sec; CPU: 0.200 sec
systime0.303953
time0.389482021332
usrtime0.014997
working_directory/project/teaser/genometeaser/tests_generated/6e77d132a218d55fc27515c6d7f3e63e

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory212604000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.164 sec; CPU: 0.113 sec
[bwa_aln_core] convert to sequence coordinate... 0.11 sec
[bwa_aln_core] refine gapped alignments... 0.02 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/D_melanogaster.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.180 sec; CPU: 0.141 sec
systime0.245962
time0.351989984512
usrtime0.012998
working_directory/project/teaser/genometeaser/tests_generated/6e77d132a218d55fc27515c6d7f3e63e

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/D_melanogaster.fasta 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/D_melanogaster.fasta reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/D_melanogaster.fasta reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
memory445820000
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... 30.14 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 179657 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq
[main] Real time: 10.612 sec; CPU: 30.663 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... 40.44 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 179657 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads2.fastq
[main] Real time: 21.021 sec; CPU: 40.803 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (110, 122, 137)
[infer_isize] low and high boundaries: 100 and 191 for estimating avg and std
[infer_isize] inferred external isize from 147888 pairs: 125.458 +/- 18.905
[infer_isize] skewness: 0.850; kurtosis: 0.201; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 251 (6.63 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.17 sec
[bwa_sai2sam_pe_core] changing coordinates of 869 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 1364 out of 5538 Q17 singletons are mated.
[bwa_paired_sw] 24 out of 76674 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.66 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 4.80 sec
[bwa_sai2sam_pe_core] print alignments... 1.00 sec
[bwa_sai2sam_pe_core] 179657 sequences have been processed.
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/D_melanogaster.fasta out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq
[main] Real time: 14.796 sec; CPU: 13.190 sec
systime0.72289
time46.4673511982
usrtime83.950237
working_directory/project/teaser/genometeaser/tests_generated/6e77d132a218d55fc27515c6d7f3e63e