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 Mapped9452694.526%
Wrongly Mapped16451.645%
Not Mapped38293.829%
Total100000100.0%
Read Failure Statistics
Not mapped38293.829%
Missing in mapper output00.0%
Mapped to wrong chromosome8620.862%
Mapped to wrong position7830.783%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.971900
Precision0.982900
Recall0.961100
Timing
Raw Mapping Time69.072s
Effective Mapping Time66.592s
Effective Init Time2.480s
Effective Time MeasureCPU
Mapping Time (Wall)37.295s
Mapping Time (CPU)69.072s
Mapping Time (CPU User)64.608s
Mapping Time (CPU System)4.464s
Init Time (Wall)2.651s
Init Time (CPU)2.480s
Init Time (CPU User)0.136s
Init Time (CPU System)2.344s
Additional Information
Mapper Memory Usage1620 MB
Total Test Runtime (Wall)215.237s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Gallus_gallus.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Gallus_gallus.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Gallus_gallus.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/Gallus_gallus.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Gallus_gallus.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Gallus_gallus.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Gallus_gallus.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory1540044000
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/Gallus_gallus.fa reads_base.fastq
[main] Real time: 89.135 sec; CPU: 1.220 sec
[bwa_aln_core] convert to sequence coordinate... 1.55 sec
[bwa_aln_core] refine gapped alignments... 0.30 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/Gallus_gallus.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 68.207 sec; CPU: 1.940 sec
systime3.024
time157.414778233
usrtime0.148
working_directory/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Gallus_gallus.fa reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/Gallus_gallus.fa out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory1540112000
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/Gallus_gallus.fa reads_base.fastq
[main] Real time: 0.869 sec; CPU: 0.848 sec
[bwa_aln_core] convert to sequence coordinate... 1.30 sec
[bwa_aln_core] refine gapped alignments... 0.24 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/Gallus_gallus.fa out_bwa.sam.bwa reads_base.fastq
[main] Real time: 1.710 sec; CPU: 1.620 sec
systime2.344
time2.65095186234
usrtime0.136
working_directory/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Gallus_gallus.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Gallus_gallus.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Gallus_gallus.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/Gallus_gallus.fa reads1.fastq -t 4 > out_bwa.sam_1.sai; /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/Gallus_gallus.fa reads2.fastq -t 4 > out_bwa.sam_2.sai; /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Gallus_gallus.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq > out_bwa.sam
memory1620020000
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... 27.55 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 50000 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Gallus_gallus.fa reads1.fastq
[main] Real time: 10.033 sec; CPU: 28.644 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... 26.51 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 50000 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/Gallus_gallus.fa reads2.fastq
[main] Real time: 10.626 sec; CPU: 27.616 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (196, 200, 204)
[infer_isize] low and high boundaries: 180 and 220 for estimating avg and std
[infer_isize] inferred external isize from 44723 pairs: 199.980 +/- 6.565
[infer_isize] skewness: 0.000; kurtosis: -0.143; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 245 (6.92 sigma)
[bwa_sai2sam_pe_core] time elapses: 2.99 sec
[bwa_sai2sam_pe_core] changing coordinates of 1 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 3 out of 3386 Q17 singletons are mated.
[bwa_paired_sw] 1 out of 45101 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 3.01 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 5.45 sec
[bwa_sai2sam_pe_core] print alignments... 0.76 sec
[bwa_sai2sam_pe_core] 50000 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa sampe /project/teaser/genometeaser/references/Gallus_gallus.fa out_bwa.sam_1.sai out_bwa.sam_2.sai reads1.fastq reads2.fastq
[main] Real time: 16.527 sec; CPU: 12.784 sec
systime4.464
time37.2950251102
usrtime64.608
working_directory/project/teaser/genometeaser/tests_generated/42fc1d552498df3b8ed5a53dd70b689a