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 Mapped45742256.724%
Wrongly Mapped596917.402%
Not Mapped28929135.874%
Total806404100.0%
Read Failure Statistics
Not mapped51620.64%
Missing in mapper output28412935.234%
Mapped to wrong chromosome352844.375%
Mapped to wrong position244073.027%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.933800
Precision0.884600
Recall0.988800
Timing
Raw Mapping Time0.000s
Effective Mapping Time0.000s
Effective Init Time425.120s
Effective Time MeasureCPU
Mapping Time (Wall)0.000s
Mapping Time (CPU)0.000s
Mapping Time (CPU User)0.000s
Mapping Time (CPU System)0.000s
Init Time (Wall)433.615s
Init Time (CPU)425.120s
Init Time (CPU User)0.324s
Init Time (CPU System)424.796s
Additional Information
Mapper Memory Usage0 MB
Total Test Runtime (Wall)2302.388s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
Errors and Warnings
TypeMessageFilePosition
Unexpectedly reached end of mapper outputsorted_out_bwa.samread.000522275
Subprocess exceeded maximum allowed runtime: /project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads.fastq > out_bwa.samNoneNone
Runtime < Init runtime, using unadjusted runtime as mapping timeNoneNone
Error occured executing pipeline main: 'memory', traceback: Traceback (most recent call last): File "/project/teaser/genometeaser/lib/test.py", line 432, in executePipeline result = script_locals[script_name](self, *args) File "tests_base/base_mapping/calc_time.py", line 42, in calc_time stats_out.memory = mapper_result["memory"] KeyError: 'memory' Test a720be7d510db33409606fe9fee515f7main
Subprocess Log

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory7090996000
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/M_musculus.fasta reads_base.fastq
[main] Real time: 412.915 sec; CPU: 177.168 sec
[bwa_aln_core] convert to sequence coordinate... 234.31 sec
[bwa_aln_core] refine gapped alignments... 44.72 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/M_musculus.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 466.809 sec; CPU: 279.036 sec
systime455.844
time879.790501833
usrtime0.38
working_directory/project/teaser/genometeaser/tests_generated/a720be7d510db33409606fe9fee515f7

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam
memory7091012000
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/M_musculus.fasta reads_base.fastq
[main] Real time: 157.926 sec; CPU: 154.836 sec
[bwa_aln_core] convert to sequence coordinate... 231.74 sec
[bwa_aln_core] refine gapped alignments... 38.51 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/M_musculus.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 275.605 sec; CPU: 270.260 sec
systime424.796
time433.615078926
usrtime0.324
working_directory/project/teaser/genometeaser/tests_generated/a720be7d510db33409606fe9fee515f7

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

command/project/teaser/genometeaser/software/bwa aln /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project/teaser/genometeaser/software/bwa samse /project/teaser/genometeaser/references/M_musculus.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam
return1
status3
stderr
stdout
systime0
time0
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/a720be7d510db33409606fe9fee515f7