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 Mapped48352996.975%
Wrongly Mapped130932.626%
Not Mapped19920.4%
Total498614100.0%
Read Failure Statistics
Not mapped19920.4%
Missing in mapper output00.0%
Mapped to wrong chromosome50261.008%
Mapped to wrong position80671.618%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.984600
Precision0.973600
Recall0.995900
Timing
Raw Mapping Time95.152s
Effective Mapping Time94.844s
Effective Init Time0.308s
Effective Time MeasureCPU
Mapping Time (Wall)60.335s
Mapping Time (CPU)95.152s
Mapping Time (CPU User)92.716s
Mapping Time (CPU System)2.436s
Init Time (Wall)0.434s
Init Time (CPU)0.308s
Init Time (CPU User)0.000s
Init Time (CPU System)0.308s
Additional Information
Mapper Memory Usage458 MB
Total Test Runtime (Wall)141.375s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 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/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory178664000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 10.332 sec; CPU: 0.144 sec
[bwa_aln_core] convert to sequence coordinate... 0.18 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: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq
[main] Real time: 8.012 sec; CPU: 0.224 sec
systime0.356
time18.4270260334
usrtime0.024
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory178796000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.141 sec; CPU: 0.104 sec
[bwa_aln_core] convert to sequence coordinate... 0.16 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/Arabidopsis_thaliana.fas out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.226 sec; CPU: 0.192 sec
systime0.308
time0.433823108673
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 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/Arabidopsis_thaliana.fas reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
memory458052000
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... 36.83 sec
[bwa_aln_core] write to the disk... 0.14 sec
[bwa_aln_core] 249307 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads1.fastq
[main] Real time: 14.897 sec; CPU: 37.804 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... 36.68 sec
[bwa_aln_core] write to the disk... 0.14 sec
[bwa_aln_core] 249307 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads2.fastq
[main] Real time: 14.956 sec; CPU: 37.672 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (80, 100, 121)
[infer_isize] low and high boundaries: 60 and 203 for estimating avg and std
[infer_isize] inferred external isize from 224593 pairs: 102.791 +/- 27.737
[infer_isize] skewness: 0.554; kurtosis: -0.234; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 285 (6.58 sigma)
[bwa_sai2sam_pe_core] time elapses: 9.48 sec
[bwa_sai2sam_pe_core] changing coordinates of 4034 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 3244 out of 4654 Q17 singletons are mated.
[bwa_paired_sw] 78 out of 27361 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.49 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 4.04 sec
[bwa_sai2sam_pe_core] print alignments... 3.07 sec
[bwa_sai2sam_pe_core] 249307 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq
[main] Real time: 30.349 sec; CPU: 19.616 sec
systime2.436
time60.3354699612
usrtime92.716
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af