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 Mapped52848588.249%
Wrongly Mapped6824711.396%
Not Mapped21260.355%
Total598858100.0%
Read Failure Statistics
Not mapped1730.029%
Missing in mapper output19530.326%
Mapped to wrong chromosome401396.703%
Mapped to wrong position281084.694%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.939200
Precision0.885600
Recall0.999700
Timing
Raw Mapping Time0.000s
Effective Mapping Time0.000s
Effective Init Time0.000s
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)0.000s
Init Time (CPU)0.000s
Init Time (CPU User)0.000s
Init Time (CPU System)0.000s
Additional Information
Mapper Memory Usage0 MB
Total Test Runtime (Wall)2773.007s
Mapper Command Line: 
/software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads.fastq --no-progress
Errors and Warnings
TypeMessageFilePosition
Unexpectedly reached end of mapper outputsorted_out_ngm_0_4_11.samread.000596905
Subprocess exceeded maximum allowed runtime: /software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progressNoneNone
Subprocess exceeded maximum allowed runtime: /software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progressNoneNone
Subprocess exceeded maximum allowed runtime: /software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads.fastq --no-progressNoneNone
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 9df2b6f30934a6f088552bf04d77f27bmain
Subprocess Log

/software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress
return1
status3
stderr
stdout
systime0
time0
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/9df2b6f30934a6f088552bf04d77f27b

/software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress
return1
status3
stderr
stdout
systime0
time0
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/9df2b6f30934a6f088552bf04d77f27b

/software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads.fastq --no-progress

command/software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads.fastq --no-progress
return1
status3
stderr
stdout
systime0
time0
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/9df2b6f30934a6f088552bf04d77f27b