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 Mapped74247794.669%
Wrongly Mapped406595.184%
Not Mapped11540.147%
Total784290100.0%
Read Failure Statistics
Not mapped11540.147%
Missing in mapper output00.0%
Mapped to wrong chromosome288893.683%
Mapped to wrong position117701.501%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.972600
Precision0.948100
Recall0.998400
Timing
Raw Mapping Time416.988s
Effective Mapping Time409.684s
Effective Init Time7.304s
Effective Time MeasureCPU
Mapping Time (Wall)285.968s
Mapping Time (CPU)416.988s
Mapping Time (CPU User)394.332s
Mapping Time (CPU System)22.656s
Init Time (Wall)7.539s
Init Time (CPU)7.304s
Init Time (CPU User)0.168s
Init Time (CPU System)7.136s
Additional Information
Mapper Memory Usage4858 MB
Total Test Runtime (Wall)847.095s
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
memory4598848000
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/H_sapiens.fa reads_base.fastq
[main] Real time: 267.104 sec; CPU: 5.648 sec
[bwa_aln_core] convert to sequence coordinate... 5.20 sec
[bwa_aln_core] refine gapped alignments... 0.93 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/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 222.253 sec; CPU: 6.132 sec
systime11.652
time489.462064028
usrtime0.136
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa

/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
memory4598756000
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... 0.06 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/H_sapiens.fa reads_base.fastq
[main] Real time: 2.839 sec; CPU: 2.772 sec
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.76 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/H_sapiens.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 4.600 sec; CPU: 4.516 sec
systime7.136
time7.5387430191
usrtime0.168
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa

/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
memory4858556000
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... 64.89 sec
[bwa_aln_core] write to the disk... 0.16 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 33.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 392145 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq
[main] Real time: 36.450 sec; CPU: 101.960 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... 62.91 sec
[bwa_aln_core] write to the disk... 0.16 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 38.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 392145 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads2.fastq
[main] Real time: 34.357 sec; CPU: 105.740 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (77, 99, 121)
[infer_isize] low and high boundaries: 40 and 209 for estimating avg and std
[infer_isize] inferred external isize from 203823 pairs: 99.623 +/- 31.142
[infer_isize] skewness: 0.258; kurtosis: -0.362; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 319 (7.04 sigma)
[bwa_sai2sam_pe_core] time elapses: 137.53 sec
[bwa_sai2sam_pe_core] changing coordinates of 22116 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 2236 out of 2573 Q17 singletons are mated.
[bwa_paired_sw] 1404 out of 9736 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.59 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.86 sec
[bwa_sai2sam_pe_core] print alignments... 2.11 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (77, 99, 121)
[infer_isize] low and high boundaries: 40 and 209 for estimating avg and std
[infer_isize] inferred external isize from 101048 pairs: 99.610 +/- 31.191
[infer_isize] skewness: 0.251; kurtosis: -0.371; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 319 (7.04 sigma)
[bwa_sai2sam_pe_core] time elapses: 62.72 sec
[bwa_sai2sam_pe_core] changing coordinates of 10889 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 1144 out of 1313 Q17 singletons are mated.
[bwa_paired_sw] 752 out of 5066 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.56 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.35 sec
[bwa_sai2sam_pe_core] print alignments... 0.67 sec
[bwa_sai2sam_pe_core] 392145 sequences have been processed.
[main] Version: 0.7.16a-r1181
[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: 214.967 sec; CPU: 209.244 sec
systime22.656
time285.967822075
usrtime394.332
working_directory/project/teaser/genometeaser/tests_generated/959fff07f73e2ad276591caaff4e83fa