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 Mapped61309531.678%
Wrongly Mapped1658938.572%
Not Mapped115638259.75%
Total1935370100.0%
Read Failure Statistics
Not mapped31910.165%
Missing in mapper output115319159.585%
Mapped to wrong chromosome1216006.283%
Mapped to wrong position442912.289%
Mapped to wrong strand20.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.878800
Precision0.787000
Recall0.994800
Timing
Raw Mapping Time0.000s
Effective Mapping Time0.000s
Effective Init Time249.644s
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)252.508s
Init Time (CPU)249.644s
Init Time (CPU User)0.092s
Init Time (CPU System)249.552s
Additional Information
Mapper Memory Usage0 MB
Total Test Runtime (Wall)2102.928s
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.000782179
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 43bdd5cc22aa7c6d1994fe8ebc8d72d4main
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
memory7091128000
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.fasta reads_base.fastq
[main] Real time: 443.084 sec; CPU: 61.472 sec
[bwa_aln_core] convert to sequence coordinate... 72.74 sec
[bwa_aln_core] refine gapped alignments... 9.94 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.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 367.294 sec; CPU: 82.688 sec
systime144.128
time810.416431904
usrtime0.096
working_directory/project/teaser/genometeaser/tests_generated/43bdd5cc22aa7c6d1994fe8ebc8d72d4

/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
memory7091136000
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.fasta reads_base.fastq
[main] Real time: 55.608 sec; CPU: 55.276 sec
[bwa_aln_core] convert to sequence coordinate... 168.64 sec
[bwa_aln_core] refine gapped alignments... 25.66 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.fasta out_bwa.sam.bwa reads_base.fastq
[main] Real time: 196.861 sec; CPU: 194.308 sec
systime249.552
time252.507664919
usrtime0.092
working_directory/project/teaser/genometeaser/tests_generated/43bdd5cc22aa7c6d1994fe8ebc8d72d4

/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/43bdd5cc22aa7c6d1994fe8ebc8d72d4