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 Mapped53952590.092%
Wrongly Mapped566729.463%
Not Mapped26610.444%
Total598858100.0%
Read Failure Statistics
Not mapped26610.444%
Missing in mapper output00.0%
Mapped to wrong chromosome314825.257%
Mapped to wrong position251904.206%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.947900
Precision0.904900
Recall0.995100
Timing
Raw Mapping Time182.520s
Effective Mapping Time179.320s
Effective Init Time3.200s
Effective Time MeasureCPU
Mapping Time (Wall)95.138s
Mapping Time (CPU)182.520s
Mapping Time (CPU User)171.420s
Mapping Time (CPU System)11.100s
Init Time (Wall)3.328s
Init Time (CPU)3.200s
Init Time (CPU User)0.008s
Init Time (CPU System)3.192s
Additional Information
Mapper Memory Usage504 MB
Total Test Runtime (Wall)204.555s
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
memory214372000
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: 12.370 sec; CPU: 0.944 sec
[bwa_aln_core] convert to sequence coordinate... 1.34 sec
[bwa_aln_core] refine gapped alignments... 0.06 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: 10.150 sec; CPU: 1.420 sec
systime2.36
time22.5685040951
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/dc51ba987f7f2a219710af74d49a4380

/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
memory214244000
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: 1.139 sec; CPU: 1.108 sec
[bwa_aln_core] convert to sequence coordinate... 2.02 sec
[bwa_aln_core] refine gapped alignments... 0.04 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: 2.134 sec; CPU: 2.080 sec
systime3.192
time3.3275809288
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/dc51ba987f7f2a219710af74d49a4380

/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
memory504312000
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... 61.29 sec
[bwa_aln_core] write to the disk... 0.11 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 8.71 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 299429 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: 21.337 sec; CPU: 72.656 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... 59.66 sec
[bwa_aln_core] write to the disk... 0.13 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 7.83 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 299429 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: 20.992 sec; CPU: 69.984 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 216528 pairs: 102.850 +/- 27.737
[infer_isize] skewness: 0.561; kurtosis: -0.217; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 286 (6.61 sigma)
[bwa_sai2sam_pe_core] time elapses: 21.71 sec
[bwa_sai2sam_pe_core] changing coordinates of 4299 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 3152 out of 4477 Q17 singletons are mated.
[bwa_paired_sw] 69 out of 26219 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.87 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 4.91 sec
[bwa_sai2sam_pe_core] print alignments... 3.59 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[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 30703 pairs: 102.740 +/- 27.667
[infer_isize] skewness: 0.560; kurtosis: -0.222; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 286 (6.61 sigma)
[bwa_sai2sam_pe_core] time elapses: 3.98 sec
[bwa_sai2sam_pe_core] changing coordinates of 589 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 438 out of 626 Q17 singletons are mated.
[bwa_paired_sw] 11 out of 3739 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.25 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.67 sec
[bwa_sai2sam_pe_core] print alignments... 0.53 sec
[bwa_sai2sam_pe_core] 299429 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: 52.672 sec; CPU: 39.812 sec
systime11.1
time95.1379170418
usrtime171.42
working_directory/project/teaser/genometeaser/tests_generated/dc51ba987f7f2a219710af74d49a4380