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 Mapped54506891.018%
Wrongly Mapped527008.8%
Not Mapped10900.182%
Total598858100.0%
Read Failure Statistics
Not mapped10900.182%
Missing in mapper output00.0%
Mapped to wrong chromosome286084.777%
Mapped to wrong position240924.023%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.953000
Precision0.911800
Recall0.998000
Timing
Raw Mapping Time202.188s
Effective Mapping Time193.056s
Effective Init Time9.132s
Effective Time MeasureCPU
Mapping Time (Wall)113.998s
Mapping Time (CPU)202.188s
Mapping Time (CPU User)175.788s
Mapping Time (CPU System)26.400s
Init Time (Wall)9.390s
Init Time (CPU)9.132s
Init Time (CPU User)0.020s
Init Time (CPU System)9.112s
Additional Information
Mapper Memory Usage503 MB
Total Test Runtime (Wall)237.641s
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
memory214260000
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: 12.361 sec; CPU: 3.372 sec
[bwa_aln_core] convert to sequence coordinate... 5.69 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: 12.858 sec; CPU: 5.772 sec
systime9.12
time25.3284301758
usrtime0.032
working_directory/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62

/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
memory214236000
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... 0.07 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: 3.523 sec; CPU: 3.448 sec
[bwa_aln_core] convert to sequence coordinate... 5.61 sec
[bwa_aln_core] refine gapped alignments... 0.05 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: 5.813 sec; CPU: 5.672 sec
systime9.112
time9.39028382301
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62

/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
memory503968000
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... 69.39 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... 9.57 sec
[bwa_aln_core] write to the disk... 0.03 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: 26.905 sec; CPU: 84.120 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... 55.02 sec
[bwa_aln_core] write to the disk... 0.19 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 9.45 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: 26.300 sec; CPU: 70.424 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (127, 149, 172)
[infer_isize] low and high boundaries: 60 and 262 for estimating avg and std
[infer_isize] inferred external isize from 215291 pairs: 149.421 +/- 32.745
[infer_isize] skewness: 0.028; kurtosis: -0.130; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 365 (6.57 sigma)
[bwa_sai2sam_pe_core] time elapses: 25.30 sec
[bwa_sai2sam_pe_core] changing coordinates of 6665 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 4458 out of 4566 Q17 singletons are mated.
[bwa_paired_sw] 72 out of 821 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.36 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 5.24 sec
[bwa_sai2sam_pe_core] print alignments... 4.08 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (127, 150, 172)
[infer_isize] low and high boundaries: 60 and 262 for estimating avg and std
[infer_isize] inferred external isize from 30729 pairs: 149.577 +/- 32.877
[infer_isize] skewness: 0.028; kurtosis: -0.150; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 366 (6.57 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.85 sec
[bwa_sai2sam_pe_core] changing coordinates of 909 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 635 out of 651 Q17 singletons are mated.
[bwa_paired_sw] 12 out of 126 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.13 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.72 sec
[bwa_sai2sam_pe_core] print alignments... 0.61 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: 60.672 sec; CPU: 47.584 sec
systime26.4
time113.998138189
usrtime175.788
working_directory/project/teaser/genometeaser/tests_generated/b705aa0185e37b61d45ed27cf2a0ba62