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 Mapped14386095.907%
Wrongly Mapped53433.562%
Not Mapped7970.531%
Total150000100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output7970.531%
Mapped to wrong chromosome00.0%
Mapped to wrong position53433.562%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment273
Secondary Alignments0
F-Measure0.981800
Precision0.964200
Recall1.000000
Timing
Raw Mapping Time468.344s
Effective Mapping Time467.976s
Effective Init Time0.368s
Effective Time MeasureCPU
Mapping Time (Wall)496.393s
Mapping Time (CPU)468.344s
Mapping Time (CPU User)451.452s
Mapping Time (CPU System)16.892s
Init Time (Wall)2.969s
Init Time (CPU)0.368s
Init Time (CPU User)0.204s
Init Time (CPU System)0.164s
Additional Information
Mapper Memory Usage91 MB
Total Test Runtime (Wall)527.460s
Mapper Command Line: 
/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/E_coli.fasta.idx -d /project/teaser/genometeaser/references/E_coli.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/E_coli.fasta.idx -d /project/teaser/genometeaser/references/E_coli.fasta -q reads_base.fastq > out_segemehl.sam

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/E_coli.fasta.idx -d /project/teaser/genometeaser/references/E_coli.fasta -q reads_base.fastq > out_segemehl.sam
memory86380000
return0
status1
stderr
None
stdout
[SEGEMEHL] Thu Aug 30 15:45:22 2018: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Thu Aug 30 15:45:22 2018: 1 query sequences found.
[SEGEMEHL] Thu Aug 30 15:45:22 2018: reading database sequences.
[SEGEMEHL] Thu Aug 30 15:45:22 2018: 1 database sequences found.
[SEGEMEHL] Thu Aug 30 15:45:22 2018: total length of db sequences: 5132068
[SEGEMEHL] Thu Aug 30 15:45:22 2018: reading suffix array '/project/teaser/genometeaser/references/E_coli.fasta.idx' from disk.
[SEGEMEHL] Thu Aug 30 15:45:23 2018: reading lcpc/vtab.
[SEGEMEHL] Thu Aug 30 15:45:23 2018: reading childtab.
[SEGEMEHL] Thu Aug 30 15:45:23 2018: reading suflinks.
[SEGEMEHL] Thu Aug 30 15:45:23 2018: reading lsint id.
[SEGEMEHL] Thu Aug 30 15:45:23 2018: read suffix array '/project/teaser/genometeaser/references/E_coli.fasta.idx' with 5132069 elements.
[SEGEMEHL] Thu Aug 30 15:45:23 2018: md5 keys of index and db match.
[SEGEMEHL] Thu Aug 30 15:45:23 2018: reading the suffix array has taken 1.000000 seconds.
[= ] 0%(0) reads matched. /
[SEGEMEHL] Thu Aug 30 15:45:23 2018: matching w/ suffixarray has taken 0.000000 seconds.
[SEGEMEHL] Thu Aug 30 15:45:23 2018:
Goodbye.
"Halt die Klappe, ich hab' Feierabend." (Schildkroede)
systime0.148
time0.498566150665
usrtime0.16
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558

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

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/E_coli.fasta.idx -d /project/teaser/genometeaser/references/E_coli.fasta -q reads_base.fastq > out_segemehl.sam
memory85472000
return0
status1
stderr
None
stdout
[SEGEMEHL] Thu Aug 30 15:45:25 2018: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Thu Aug 30 15:45:26 2018: 1 query sequences found.
[SEGEMEHL] Thu Aug 30 15:45:26 2018: reading database sequences.
[SEGEMEHL] Thu Aug 30 15:45:26 2018: 1 database sequences found.
[SEGEMEHL] Thu Aug 30 15:45:26 2018: total length of db sequences: 5132068
[SEGEMEHL] Thu Aug 30 15:45:26 2018: reading suffix array '/project/teaser/genometeaser/references/E_coli.fasta.idx' from disk.
[SEGEMEHL] Thu Aug 30 15:45:26 2018: reading lcpc/vtab.
[SEGEMEHL] Thu Aug 30 15:45:26 2018: reading childtab.
[SEGEMEHL] Thu Aug 30 15:45:26 2018: reading suflinks.
[SEGEMEHL] Thu Aug 30 15:45:26 2018: reading lsint id.
[SEGEMEHL] Thu Aug 30 15:45:26 2018: read suffix array '/project/teaser/genometeaser/references/E_coli.fasta.idx' with 5132069 elements.
[SEGEMEHL] Thu Aug 30 15:45:26 2018: md5 keys of index and db match.
[SEGEMEHL] Thu Aug 30 15:45:26 2018: reading the suffix array has taken 0.000000 seconds.
[= ] 0%(0) reads matched. /
[SEGEMEHL] Thu Aug 30 15:45:26 2018: matching w/ suffixarray has taken 0.000000 seconds.
[SEGEMEHL] Thu Aug 30 15:45:26 2018:
Goodbye.
"Ick fahr nur noch die janz jrossen Poette, wa!" (Apotheker Lenz)
systime0.164
time2.96945905685
usrtime0.204
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558

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

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/E_coli.fasta.idx -d /project/teaser/genometeaser/references/E_coli.fasta -q reads.fastq > out_segemehl.sam
memory91348000
return0
status1
stderr
None
stdout
[SEGEMEHL] Thu Aug 30 15:45:26 2018: reading queries in 'reads.fastq'.
[SEGEMEHL] Thu Aug 30 15:45:28 2018: 150000 query sequences found.
[SEGEMEHL] Thu Aug 30 15:45:28 2018: reading database sequences.
[SEGEMEHL] Thu Aug 30 15:45:28 2018: 1 database sequences found.
[SEGEMEHL] Thu Aug 30 15:45:28 2018: total length of db sequences: 5132068
[SEGEMEHL] Thu Aug 30 15:45:28 2018: reading suffix array '/project/teaser/genometeaser/references/E_coli.fasta.idx' from disk.
[SEGEMEHL] Thu Aug 30 15:45:28 2018: reading lcpc/vtab.
[SEGEMEHL] Thu Aug 30 15:45:28 2018: reading childtab.
[SEGEMEHL] Thu Aug 30 15:45:28 2018: reading suflinks.
[SEGEMEHL] Thu Aug 30 15:45:28 2018: reading lsint id.
[SEGEMEHL] Thu Aug 30 15:45:28 2018: read suffix array '/project/teaser/genometeaser/references/E_coli.fasta.idx' with 5132069 elements.
[SEGEMEHL] Thu Aug 30 15:45:28 2018: md5 keys of index and db match.
[SEGEMEHL] Thu Aug 30 15:45:28 2018: reading the suffix array has taken 0.000000 seconds.
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systime16.892
time496.392861843
usrtime451.452
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558