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 Mapped31204191.095%
Wrongly Mapped303958.873%
Not Mapped1060.031%
Total342543100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output1060.031%
Mapped to wrong chromosome166524.861%
Mapped to wrong position137434.012%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.953600
Precision0.911200
Recall1.000000
Timing
Raw Mapping Time0.000s
Effective Mapping Time0.000s
Effective Init Time11.272s
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)11.338s
Init Time (CPU)11.272s
Init Time (CPU User)8.444s
Init Time (CPU System)2.828s
Additional Information
Mapper Memory Usage0 MB
Total Test Runtime (Wall)1151.302s
Mapper Command Line: 
/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/D_melanogaster.fasta.idx -d /project/teaser/genometeaser/references/D_melanogaster.fasta -q reads1.fastq -p reads2.fastq > out_segemehl.sam
Errors and Warnings
TypeMessageFilePosition
Subprocess exceeded maximum allowed runtime: /project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/D_melanogaster.fasta.idx -d /project/teaser/genometeaser/references/D_melanogaster.fasta -q reads1.fastq -p reads2.fastq > out_segemehl.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 4cb6b18a4da1297d4cf7e8f8ca244517main
Subprocess Log

/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/D_melanogaster.fasta.idx -d /project/teaser/genometeaser/references/D_melanogaster.fasta -q reads_base.fastq > out_segemehl.sam

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/D_melanogaster.fasta.idx -d /project/teaser/genometeaser/references/D_melanogaster.fasta -q reads_base.fastq > out_segemehl.sam
memory2341476000
return0
status1
stderr
None
stdout
[SEGEMEHL] Thu Nov  8 00:49:48 2018: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Thu Nov 8 00:49:48 2018: 1 query sequences found.
[SEGEMEHL] Thu Nov 8 00:49:48 2018: reading database sequences.
[SEGEMEHL] Thu Nov 8 00:50:01 2018: 1870 database sequences found.
[SEGEMEHL] Thu Nov 8 00:50:01 2018: total length of db sequences: 143725995
[SEGEMEHL] Thu Nov 8 00:50:01 2018: reading suffix array '/project/teaser/genometeaser/references/D_melanogaster.fasta.idx' from disk.
[SEGEMEHL] Thu Nov 8 00:50:51 2018: reading lcpc/vtab.
[SEGEMEHL] Thu Nov 8 00:51:09 2018: reading childtab.
[SEGEMEHL] Thu Nov 8 00:51:58 2018: reading suflinks.
[SEGEMEHL] Thu Nov 8 00:52:59 2018: reading lsint id.
[SEGEMEHL] Thu Nov 8 00:53:00 2018: read suffix array '/project/teaser/genometeaser/references/D_melanogaster.fasta.idx' with 143727865 elements.
[SEGEMEHL] Thu Nov 8 00:53:01 2018: md5 keys of index and db match.
[SEGEMEHL] Thu Nov 8 00:53:01 2018: reading the suffix array has taken 180.000000 seconds.
[= ] 0%(0) reads matched. /
[SEGEMEHL] Thu Nov 8 00:53:01 2018: matching w/ suffixarray has taken 0.000000 seconds.
[SEGEMEHL] Thu Nov 8 00:53:01 2018:
Goodbye.
"Die Ficker!" (Thommy)
systime4.708
time193.04320097
usrtime7.856
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517

/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/D_melanogaster.fasta.idx -d /project/teaser/genometeaser/references/D_melanogaster.fasta -q reads_base.fastq > out_segemehl.sam

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/D_melanogaster.fasta.idx -d /project/teaser/genometeaser/references/D_melanogaster.fasta -q reads_base.fastq > out_segemehl.sam
memory2342312000
return0
status1
stderr
None
stdout
[SEGEMEHL] Thu Nov  8 00:53:01 2018: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Thu Nov 8 00:53:01 2018: 1 query sequences found.
[SEGEMEHL] Thu Nov 8 00:53:01 2018: reading database sequences.
[SEGEMEHL] Thu Nov 8 00:53:09 2018: 1870 database sequences found.
[SEGEMEHL] Thu Nov 8 00:53:09 2018: total length of db sequences: 143725995
[SEGEMEHL] Thu Nov 8 00:53:09 2018: reading suffix array '/project/teaser/genometeaser/references/D_melanogaster.fasta.idx' from disk.
[SEGEMEHL] Thu Nov 8 00:53:10 2018: reading lcpc/vtab.
[SEGEMEHL] Thu Nov 8 00:53:11 2018: reading childtab.
[SEGEMEHL] Thu Nov 8 00:53:11 2018: reading suflinks.
[SEGEMEHL] Thu Nov 8 00:53:12 2018: reading lsint id.
[SEGEMEHL] Thu Nov 8 00:53:12 2018: read suffix array '/project/teaser/genometeaser/references/D_melanogaster.fasta.idx' with 143727865 elements.
[SEGEMEHL] Thu Nov 8 00:53:13 2018: md5 keys of index and db match.
[SEGEMEHL] Thu Nov 8 00:53:13 2018: reading the suffix array has taken 4.000000 seconds.
[= ] 0%(0) reads matched. /
[SEGEMEHL] Thu Nov 8 00:53:13 2018: matching w/ suffixarray has taken 0.000000 seconds.
[SEGEMEHL] Thu Nov 8 00:53:13 2018:
Goodbye.
"Wir sind hier nicht in Seattle Dirk!" (Tocotronic)
systime2.828
time11.3378829956
usrtime8.444
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517

/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/D_melanogaster.fasta.idx -d /project/teaser/genometeaser/references/D_melanogaster.fasta -q reads1.fastq -p reads2.fastq > out_segemehl.sam

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/D_melanogaster.fasta.idx -d /project/teaser/genometeaser/references/D_melanogaster.fasta -q reads1.fastq -p reads2.fastq > out_segemehl.sam
return1
status3
stderr
stdout
systime0
time0
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/4cb6b18a4da1297d4cf7e8f8ca244517