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 Mapped64957190.39%
Wrongly Mapped679509.456%
Not Mapped11070.154%
Total718628100.0%
Read Failure Statistics
Not mapped11070.154%
Missing in mapper output00.0%
Mapped to wrong chromosome374355.209%
Mapped to wrong position305154.246%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.949500
Precision0.905300
Recall0.998300
Timing
Raw Mapping Time136.260s
Effective Mapping Time135.892s
Effective Init Time0.368s
Effective Time MeasureCPU
Mapping Time (Wall)88.391s
Mapping Time (CPU)136.260s
Mapping Time (CPU User)132.928s
Mapping Time (CPU System)3.332s
Init Time (Wall)0.476s
Init Time (CPU)0.368s
Init Time (CPU User)0.032s
Init Time (CPU System)0.336s
Additional Information
Mapper Memory Usage479 MB
Total Test Runtime (Wall)175.897s
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
memory214416000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.156 sec; CPU: 0.128 sec
[bwa_aln_core] convert to sequence coordinate... 0.19 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: 0.7.16a-r1181
[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: 0.284 sec; CPU: 0.240 sec
systime0.364
time0.488878011703
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/e36fcf554e99e1f3a2b5fd499196eaa6

/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
memory214416000
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/D_melanogaster.fasta reads_base.fastq
[main] Real time: 0.148 sec; CPU: 0.124 sec
[bwa_aln_core] convert to sequence coordinate... 0.19 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: 0.7.16a-r1181
[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: 0.267 sec; CPU: 0.236 sec
systime0.336
time0.476260900497
usrtime0.032
working_directory/project/teaser/genometeaser/tests_generated/e36fcf554e99e1f3a2b5fd499196eaa6

/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
memory479380000
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... 38.03 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... 11.86 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 359314 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads1.fastq
[main] Real time: 19.047 sec; CPU: 51.300 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... 34.95 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... 12.52 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 359314 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/D_melanogaster.fasta reads2.fastq
[main] Real time: 19.211 sec; CPU: 48.864 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (107, 129, 152)
[infer_isize] low and high boundaries: 50 and 242 for estimating avg and std
[infer_isize] inferred external isize from 214812 pairs: 129.409 +/- 32.536
[infer_isize] skewness: 0.068; kurtosis: -0.229; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 343 (6.58 sigma)
[bwa_sai2sam_pe_core] time elapses: 20.00 sec
[bwa_sai2sam_pe_core] changing coordinates of 6439 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 3464 out of 3612 Q17 singletons are mated.
[bwa_paired_sw] 89 out of 1920 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.44 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 2.27 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (107, 130, 152)
[infer_isize] low and high boundaries: 50 and 242 for estimating avg and std
[infer_isize] inferred external isize from 79684 pairs: 129.507 +/- 32.433
[infer_isize] skewness: 0.055; kurtosis: -0.208; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 343 (6.58 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.53 sec
[bwa_sai2sam_pe_core] changing coordinates of 2482 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 1273 out of 1331 Q17 singletons are mated.
[bwa_paired_sw] 32 out of 737 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.21 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.02 sec
[bwa_sai2sam_pe_core] print alignments... 1.35 sec
[bwa_sai2sam_pe_core] 359314 sequences have been processed.
[main] Version: 0.7.16a-r1181
[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: 50.006 sec; CPU: 36.048 sec
systime3.332
time88.3905949593
usrtime132.928
working_directory/project/teaser/genometeaser/tests_generated/e36fcf554e99e1f3a2b5fd499196eaa6