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 Mapped16873194.778%
Wrongly Mapped26931.513%
Not Mapped66043.71%
Total178028100.0%
Read Failure Statistics
Not mapped66043.71%
Missing in mapper output00.0%
Mapped to wrong chromosome18731.052%
Mapped to wrong position8200.461%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.973200
Precision0.984300
Recall0.962300
Timing
Raw Mapping Time344.412s
Effective Mapping Time338.912s
Effective Init Time5.500s
Effective Time MeasureCPU
Mapping Time (Wall)126.554s
Mapping Time (CPU)344.412s
Mapping Time (CPU User)326.068s
Mapping Time (CPU System)18.344s
Init Time (Wall)5.629s
Init Time (CPU)5.500s
Init Time (CPU User)0.152s
Init Time (CPU System)5.348s
Additional Information
Mapper Memory Usage4060 MB
Total Test Runtime (Wall)567.989s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Bos_taurus.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Bos_taurus.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Bos_taurus.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/Bos_taurus.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Bos_taurus.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Bos_taurus.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory3916880000
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... 0.08 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq
[main] Real time: 237.795 sec; CPU: 3.192 sec
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.81 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Bos_taurus.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 178.575 sec; CPU: 4.172 sec
systime7.22
time416.410460949
usrtime0.156
working_directory/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Bos_taurus.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory3916884000
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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Bos_taurus.fa reads_base.fastq
[main] Real time: 1.646 sec; CPU: 1.612 sec
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.66 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 1 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Bos_taurus.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 3.929 sec; CPU: 3.872 sec
systime5.348
time5.6291179657
usrtime0.152
working_directory/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Bos_taurus.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Bos_taurus.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Bos_taurus.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/Bos_taurus.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Bos_taurus.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Bos_taurus.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
memory4060216000
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... 154.02 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89014 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Bos_taurus.fa reads1.fastq
[main] Real time: 44.638 sec; CPU: 156.632 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... 158.55 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 89014 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Bos_taurus.fa reads2.fastq
[main] Real time: 45.588 sec; CPU: 161.136 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (178, 199, 221)
[infer_isize] low and high boundaries: 150 and 307 for estimating avg and std
[infer_isize] inferred external isize from 79540 pairs: 200.902 +/- 29.706
[infer_isize] skewness: 0.409; kurtosis: -0.297; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 408 (6.98 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.02 sec
[bwa_sai2sam_pe_core] changing coordinates of 35 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 164 out of 6136 Q17 singletons are mated.
[bwa_paired_sw] 9 out of 75786 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 6.77 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 9.53 sec
[bwa_sai2sam_pe_core] print alignments... 1.34 sec
[bwa_sai2sam_pe_core] 89014 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Bos_taurus.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq
[main] Real time: 36.220 sec; CPU: 26.600 sec
systime18.344
time126.554179907
usrtime326.068
working_directory/project/teaser/genometeaser/tests_generated/14e5e97d9d3c2238f7310baab576d567