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 Mapped29479998.266%
Wrongly Mapped51931.731%
Not Mapped80.003%
Total300000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output80.003%
Mapped to wrong chromosome41571.386%
Mapped to wrong position10360.345%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.991300
Precision0.982700
Recall1.000000
Timing
Raw Mapping Time129.564s
Effective Mapping Time128.596s
Effective Init Time0.968s
Effective Time MeasureCPU
Mapping Time (Wall)157.673s
Mapping Time (CPU)129.564s
Mapping Time (CPU User)105.780s
Mapping Time (CPU System)23.784s
Init Time (Wall)1.732s
Init Time (CPU)0.968s
Init Time (CPU User)0.652s
Init Time (CPU System)0.316s
Additional Information
Mapper Memory Usage200 MB
Total Test Runtime (Wall)229.489s
Mapper Command Line: 
/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.idx -d /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta -q reads.fastq > out_segemehl.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

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

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.idx -d /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta -q reads_base.fastq > out_segemehl.sam
memory199636000
return0
status1
stderr
None
stdout
[SEGEMEHL] Mon Sep  3 13:51:31 2018: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Mon Sep 3 13:51:31 2018: 1 query sequences found.
[SEGEMEHL] Mon Sep 3 13:51:31 2018: reading database sequences.
[SEGEMEHL] Mon Sep 3 13:51:32 2018: 17 database sequences found.
[SEGEMEHL] Mon Sep 3 13:51:32 2018: total length of db sequences: 12157105
[SEGEMEHL] Mon Sep 3 13:51:32 2018: reading suffix array '/project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.idx' from disk.
[SEGEMEHL] Mon Sep 3 13:51:38 2018: reading lcpc/vtab.
[SEGEMEHL] Mon Sep 3 13:51:39 2018: reading childtab.
[SEGEMEHL] Mon Sep 3 13:51:44 2018: reading suflinks.
[SEGEMEHL] Mon Sep 3 13:51:50 2018: reading lsint id.
[SEGEMEHL] Mon Sep 3 13:51:50 2018: read suffix array '/project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.idx' with 12157122 elements.
[SEGEMEHL] Mon Sep 3 13:51:51 2018: md5 keys of index and db match.
[SEGEMEHL] Mon Sep 3 13:51:51 2018: reading the suffix array has taken 19.000000 seconds.
[= ] 0%(0) reads matched. /
[SEGEMEHL] Mon Sep 3 13:51:51 2018: matching w/ suffixarray has taken 0.000000 seconds.
[SEGEMEHL] Mon Sep 3 13:51:51 2018:
Goodbye.
"Die Ficker!" (Thommy)
systime0.512
time19.3595840931
usrtime0.812
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972

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

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.idx -d /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta -q reads_base.fastq > out_segemehl.sam
memory199296000
return0
status1
stderr
None
stdout
[SEGEMEHL] Mon Sep  3 13:51:51 2018: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Mon Sep 3 13:51:51 2018: 1 query sequences found.
[SEGEMEHL] Mon Sep 3 13:51:51 2018: reading database sequences.
[SEGEMEHL] Mon Sep 3 13:51:52 2018: 17 database sequences found.
[SEGEMEHL] Mon Sep 3 13:51:52 2018: total length of db sequences: 12157105
[SEGEMEHL] Mon Sep 3 13:51:52 2018: reading suffix array '/project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.idx' from disk.
[SEGEMEHL] Mon Sep 3 13:51:52 2018: reading lcpc/vtab.
[SEGEMEHL] Mon Sep 3 13:51:52 2018: reading childtab.
[SEGEMEHL] Mon Sep 3 13:51:52 2018: reading suflinks.
[SEGEMEHL] Mon Sep 3 13:51:52 2018: reading lsint id.
[SEGEMEHL] Mon Sep 3 13:51:52 2018: read suffix array '/project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.idx' with 12157122 elements.
[SEGEMEHL] Mon Sep 3 13:51:53 2018: md5 keys of index and db match.
[SEGEMEHL] Mon Sep 3 13:51:53 2018: reading the suffix array has taken 1.000000 seconds.
[= ] 0%(0) reads matched. /
[SEGEMEHL] Mon Sep 3 13:51:53 2018: matching w/ suffixarray has taken 0.000000 seconds.
[SEGEMEHL] Mon Sep 3 13:51:53 2018:
Goodbye.
"Mahlzeit!" (Ditsche, Ingo, Schildkroede)
systime0.316
time1.7316570282
usrtime0.652
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972

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

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.idx -d /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta -q reads.fastq > out_segemehl.sam
memory200436000
return0
status1
stderr
None
stdout
[SEGEMEHL] Mon Sep  3 13:51:53 2018: reading queries in 'reads.fastq'.
[SEGEMEHL] Mon Sep 3 13:51:56 2018: 300000 query sequences found.
[SEGEMEHL] Mon Sep 3 13:51:56 2018: reading database sequences.
[SEGEMEHL] Mon Sep 3 13:51:56 2018: 17 database sequences found.
[SEGEMEHL] Mon Sep 3 13:51:56 2018: total length of db sequences: 12157105
[SEGEMEHL] Mon Sep 3 13:51:56 2018: reading suffix array '/project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.idx' from disk.
[SEGEMEHL] Mon Sep 3 13:51:57 2018: reading lcpc/vtab.
[SEGEMEHL] Mon Sep 3 13:51:57 2018: reading childtab.
[SEGEMEHL] Mon Sep 3 13:51:57 2018: reading suflinks.
[SEGEMEHL] Mon Sep 3 13:51:57 2018: reading lsint id.
[SEGEMEHL] Mon Sep 3 13:51:57 2018: read suffix array '/project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta.idx' with 12157122 elements.
[SEGEMEHL] Mon Sep 3 13:51:57 2018: md5 keys of index and db match.
[SEGEMEHL] Mon Sep 3 13:51:57 2018: reading the suffix array has taken 1.000000 seconds.
[= ] 0%(0) reads matched. /
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[= ] 0%(150) reads matched. /
[=
systime23.784
time157.672574997
usrtime105.78
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972