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 Mapped00.0%
Wrongly Mapped00.0%
Not Mapped149993100.0%
Total149993100.0%
Read Failure Statistics
Not mapped149993100.0%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position00.0%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment7
Secondary Alignments0
F-Measure0.000000
Precision0.000000
Recall0.000000
Timing
Raw Mapping Time11.396s
Effective Mapping Time11.332s
Effective Init Time0.064s
Effective Time MeasureCPU
Mapping Time (Wall)15.641s
Mapping Time (CPU)11.396s
Mapping Time (CPU User)10.092s
Mapping Time (CPU System)1.304s
Init Time (Wall)0.214s
Init Time (CPU)0.064s
Init Time (CPU User)0.008s
Init Time (CPU System)0.056s
Additional Information
Mapper Memory Usage148 MB
Total Test Runtime (Wall)44.386s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/E_coli.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/E_coli.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/E_coli.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory21068000
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/E_coli.fasta reads_base.fastq
[main] Real time: 0.746 sec; CPU: 0.032 sec
[bwa_aln_core] convert to sequence coordinate... 0.03 sec
[bwa_aln_core] refine gapped alignments... 0.01 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/E_coli.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 1.309 sec; CPU: 0.040 sec
systime0.08
time2.10861706734
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/E_coli.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory21068000
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/E_coli.fasta reads_base.fastq
[main] Real time: 0.060 sec; CPU: 0.020 sec
[bwa_aln_core] convert to sequence coordinate... 0.03 sec
[bwa_aln_core] refine gapped alignments... 0.00 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/E_coli.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 0.090 sec; CPU: 0.036 sec
systime0.056
time0.213698148727
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/E_coli.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/E_coli.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
memory148636000
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... 8.47 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 150000 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa aln -t 4 /project/teaser/genometeaser/references/E_coli.fasta reads.fastq
[main] Real time: 5.259 sec; CPU: 9.632 sec
[bwa_aln_core] convert to sequence coordinate... 0.07 sec
[bwa_aln_core] refine gapped alignments... 0.14 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 150000 sequences have been processed.
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/E_coli.fasta out_bwa.sam.bwa reads.fastq
[main] Real time: 10.264 sec; CPU: 1.704 sec
systime1.304
time15.640860796
usrtime10.092
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923