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 Mapped15373986.429%
Wrongly Mapped126507.112%
Not Mapped114896.459%
Total177878100.0%
Read Failure Statistics
Not mapped114896.459%
Missing in mapper output00.0%
Mapped to wrong chromosome64343.617%
Mapped to wrong position62163.495%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.927200
Precision0.924000
Recall0.930500
Timing
Raw Mapping Time178.664s
Effective Mapping Time172.160s
Effective Init Time6.504s
Effective Time MeasureCPU
Mapping Time (Wall)81.585s
Mapping Time (CPU)178.664s
Mapping Time (CPU User)166.808s
Mapping Time (CPU System)11.856s
Init Time (Wall)6.739s
Init Time (CPU)6.504s
Init Time (CPU User)0.020s
Init Time (CPU System)6.484s
Additional Information
Mapper Memory Usage388 MB
Total Test Runtime (Wall)149.675s
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
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: 12.379 sec; CPU: 4.924 sec
[bwa_aln_core] convert to sequence coordinate... 5.54 sec
[bwa_aln_core] refine gapped alignments... 0.07 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: 12.704 sec; CPU: 5.620 sec
systime10.536
time25.1256959438
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f

/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
memory214460000
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: 2.532 sec; CPU: 2.464 sec
[bwa_aln_core] convert to sequence coordinate... 3.97 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: 4.128 sec; CPU: 4.028 sec
systime6.484
time6.7386238575
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f

/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
memory388808000
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... 68.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 88939 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: 24.005 sec; CPU: 70.796 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... 80.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 88939 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: 24.909 sec; CPU: 83.496 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (280, 302, 324)
[infer_isize] low and high boundaries: 202 and 412 for estimating avg and std
[infer_isize] inferred external isize from 68552 pairs: 301.992 +/- 32.805
[infer_isize] skewness: -0.009; kurtosis: -0.106; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 516 (6.52 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.45 sec
[bwa_sai2sam_pe_core] changing coordinates of 48 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 110 out of 9339 Q17 singletons are mated.
[bwa_paired_sw] 67 out of 70464 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 4.77 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 9.99 sec
[bwa_sai2sam_pe_core] print alignments... 0.92 sec
[bwa_sai2sam_pe_core] 88939 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: 32.548 sec; CPU: 24.312 sec
systime11.856
time81.5853569508
usrtime166.808
working_directory/project/teaser/genometeaser/tests_generated/e06f9a576d69697f7ad166f2c53eac4f