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 Mapped24553790.088%
Wrongly Mapped219878.067%
Not Mapped50291.845%
Total272553100.0%
Read Failure Statistics
Not mapped50291.845%
Missing in mapper output00.0%
Mapped to wrong chromosome107063.928%
Mapped to wrong position112814.139%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.947900
Precision0.917800
Recall0.979900
Timing
Raw Mapping Time233.932s
Effective Mapping Time225.240s
Effective Init Time8.692s
Effective Time MeasureCPU
Mapping Time (Wall)92.596s
Mapping Time (CPU)233.932s
Mapping Time (CPU User)215.680s
Mapping Time (CPU System)18.252s
Init Time (Wall)8.873s
Init Time (CPU)8.692s
Init Time (CPU User)0.188s
Init Time (CPU System)8.504s
Additional Information
Mapper Memory Usage4150 MB
Total Test Runtime (Wall)4850.637s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa index /project/teaser/genometeaser/references/M_musculus_cutf.fasta

command/project/teaser/genometeaser/software/bwa index /project/teaser/genometeaser/references/M_musculus_cutf.fasta
return1
status1
stderr
None
stdout
[bwa_index] Pack FASTA... 72.49 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=5451075338, availableWord=395557796
[BWTIncConstructFromPacked] 10 iterations done. 99999994 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999994 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 299999994 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 399999994 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 499999994 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 599999994 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 699999994 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 799999994 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 899999994 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 999999994 characters processed.
[BWTIncConstructFromPacked] 110 iterations done. 1099999994 characters processed.
[BWTIncConstructFromPacked] 120 iterations done. 1199999994 characters processed.
[BWTIncConstructFromPacked] 130 iterations done. 1299999994 characters processed.
[BWTIncConstructFromPacked] 140 iterations done. 1399999994 characters processed.
[BWTIncConstructFromPacked] 150 iterations done. 1499999994 characters processed.
[BWTIncConstructFromPacked] 160 iterations done. 1599999994 characters processed.
[BWTIncConstructFromPacked] 170 iterations done. 1699999994 characters processed.
[BWTIncConstructFromPacked] 180 iterations done. 1799999994 characters processed.
[BWTIncConstructFromPacked] 190 iterations done. 1899999994 characters processed.
[BWTIncConstructFromPacked] 200 iterations done. 1999999994 characters processed.
[BWTIncConstructFromPacked] 210 iterations done. 2099999994 characters processed.
[BWTIncConstructFromPacked] 220 iterations done. 2199999994 characters processed.
[BWTIncConstructFromPacked] 230 iterations done. 2299999994 characters processed.
[BWTIncConstructFromPacked] 240 iterations done. 2399999994 characters processed.
[BWTIncConstructFromPacked] 250 iterations done. 2499999994 characters processed.
[BWTIncConstructFromPacked] 260 iterations done. 2599999994 characters processed.
[BWTIncConstructFromPacked] 270 iterations done. 2699999994 characters processed.
[BWTIncConstructFromPacked] 280 iterations done. 2799999994 characters processed.
[BWTIncConstructFromPacked] 290 iterations done. 2899999994 characters processed.
[BWTIncConstructFromPacked] 300 iterations done. 2999999994 characters processed.
[BWTIncConstructFromPacked] 310 iterations done. 3099999994 characters processed.
[BWTIncConstructFromPacked] 320 iterations done. 3199999994 characters processed.
[BWTIncConstructFromPacked] 330 iterations done. 3299999994 characters processed.
[BWTIncConstructFromPacked] 340 iterations done. 3399999994 characters processed.
[BWTIncConstructFromPacked] 350 iterations done. 3499999994 characters processed.
[BWTIncConstructFromPacked] 360 iterations done. 3599999994 characters processed.
[BWTIncConstructFromPacked] 370 iterations done. 3699999994 characters processed.
[BWTIncConstructFromPacked] 380 iterations done. 3799999994 characters processed.
[BWTIncConstructFromPacked] 390 iterations done. 3899999994 characters processed.
[BWTIncConstructFromPacked] 400 iterations done. 3999999994 characters processed.
[BWTIncConstructFromPacked] 410 iterations done. 4099999994 characters processed.
[BWTIncConstructFromPacked] 420 iterations done. 4199999994 characters processed.
[BWTIncConstructFromPacked] 430 iterations done. 4299999994 characters processed.
[BWTIncConstructFromPacked] 440 iterations done. 4399999994 characters processed.
[BWTIncConstructFromPacked] 450 iterations done. 4499999994 characters processed.
[BWTIncConstructFromPacked] 460 iterations done. 4599999994 characters processed.
[BWTIncConstructFromPacked] 470 iterations done. 4699999994 characters processed.
[BWTIncConstructFromPacked] 480 iterations done. 4799664682 characters processed.
[BWTIncConstructFromPacked] 490 iterations done. 4891322586 characters processed.
[BWTIncConstructFromPacked] 500 iterations done. 4972784378 characters processed.
[BWTIncConstructFromPacked] 510 iterations done. 5045183802 characters processed.
[BWTIncConstructFromPacked] 520 iterations done. 5109528586 characters processed.
[BWTIncConstructFromPacked] 530 iterations done. 5166714378 characters processed.
[BWTIncConstructFromPacked] 540 iterations done. 5217537242 characters processed.
[BWTIncConstructFromPacked] 550 iterations done. 5262704698 characters processed.
[BWTIncConstructFromPacked] 560 iterations done. 5302845626 characters processed.
[BWTIncConstructFromPacked] 570 iterations done. 5338518970 characters processed.
[BWTIncConstructFromPacked] 580 iterations done. 5370221514 characters processed.
[BWTIncConstructFromPacked] 590 iterations done. 5398394762 characters processed.
[BWTIncConstructFromPacked] 600 iterations done. 5423431210 characters processed.
[BWTIncConstructFromPacked] 610 iterations done. 5445679594 characters processed.
[bwt_gen] Finished constructing BWT in 613 iterations.
[bwa_index] 2946.09 seconds elapse.
[bwa_index] Update BWT... 29.61 sec
[bwa_index] Pack forward-only FASTA... 24.17 sec
[bwa_index] Construct SA from BWT and Occ... 979.47 sec
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa index /project/teaser/genometeaser/references/M_musculus_cutf.fasta
[main] Real time: 4697.709 sec; CPU: 4051.856 sec
systime0
time4697.71531916
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory3996028000
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/M_musculus_cutf.fasta reads_base.fastq
[main] Real time: 2.195 sec; CPU: 2.128 sec
[bwa_aln_core] convert to sequence coordinate... 4.28 sec
[bwa_aln_core] refine gapped alignments... 0.75 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/M_musculus_cutf.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 5.108 sec; CPU: 5.036 sec
systime7.044
time7.52763795853
usrtime0.136
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory3996056000
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/M_musculus_cutf.fasta reads_base.fastq
[main] Real time: 3.109 sec; CPU: 3.048 sec
[bwa_aln_core] convert to sequence coordinate... 4.84 sec
[bwa_aln_core] refine gapped alignments... 0.79 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/M_musculus_cutf.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 5.713 sec; CPU: 5.632 sec
systime8.504
time8.87325191498
usrtime0.188
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory4150244000
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... 197.21 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... 10.05 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 272553 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq
[main] Real time: 62.301 sec; CPU: 210.928 sec
[bwa_aln_core] convert to sequence coordinate... 6.94 sec
[bwa_aln_core] refine gapped alignments... 6.85 sec
[bwa_aln_core] print alignments... 1.73 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 5.07 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 0.06 sec
[bwa_aln_core] 272553 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus_cutf.fasta out_bwa.sam.bwa reads.fastq
[main] Real time: 30.198 sec; CPU: 22.956 sec
systime18.252
time92.5957589149
usrtime215.68
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d