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 Mapped00.0%
Wrongly Mapped00.0%
Not Mapped149993100.0%
Total149993100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output149993100.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position00.0%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.000000
Precision0.000000
Recall0.000000
Timing
Raw Mapping Time798.100s
Effective Mapping Time797.572s
Effective Init Time0.528s
Effective Time MeasureCPU
Mapping Time (Wall)828.516s
Mapping Time (CPU)798.100s
Mapping Time (CPU User)781.908s
Mapping Time (CPU System)16.192s
Init Time (Wall)0.816s
Init Time (CPU)0.528s
Init Time (CPU User)0.344s
Init Time (CPU System)0.184s
Additional Information
Mapper Memory Usage90 MB
Total Test Runtime (Wall)844.946s
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
TypeMessageFilePosition
Unexpectedly reached end of mapper outputsorted_out_segemehl.samY29udGlnXzc0MDA0N18xXzBfMF8wXzBfMTA3OjA6MV8wOjA6MF9hZmVm
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
memory85540000
return0
status1
stderr
None
stdout
[SEGEMEHL] Thu Aug 30 14:28:39 2018: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Thu Aug 30 14:28:39 2018: 1 query sequences found.
[SEGEMEHL] Thu Aug 30 14:28:39 2018: reading database sequences.
[SEGEMEHL] Thu Aug 30 14:28:40 2018: 1 database sequences found.
[SEGEMEHL] Thu Aug 30 14:28:40 2018: total length of db sequences: 5132068
[SEGEMEHL] Thu Aug 30 14:28:40 2018: reading suffix array '/project/teaser/genometeaser/references/E_coli.fasta.idx' from disk.
[SEGEMEHL] Thu Aug 30 14:28:43 2018: reading lcpc/vtab.
[SEGEMEHL] Thu Aug 30 14:28:44 2018: reading childtab.
[SEGEMEHL] Thu Aug 30 14:28:46 2018: reading suflinks.
[SEGEMEHL] Thu Aug 30 14:28:49 2018: reading lsint id.
[SEGEMEHL] Thu Aug 30 14:28:49 2018: read suffix array '/project/teaser/genometeaser/references/E_coli.fasta.idx' with 5132069 elements.
[SEGEMEHL] Thu Aug 30 14:28:49 2018: md5 keys of index and db match.
[SEGEMEHL] Thu Aug 30 14:28:49 2018: reading the suffix array has taken 9.000000 seconds.
[= ] 0%(0) reads matched. /
[SEGEMEHL] Thu Aug 30 14:28:49 2018: matching w/ suffixarray has taken 0.000000 seconds.
[SEGEMEHL] Thu Aug 30 14:28:49 2018:
Goodbye.
"Ich hol' jetzt die Hilti!" (Ein verzweifelter Bauarbeiter)
systime0.228
time9.21460580826
usrtime0.192
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923

/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
memory87316000
return0
status1
stderr
None
stdout
[SEGEMEHL] Thu Aug 30 14:28:50 2018: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Thu Aug 30 14:28:50 2018: 1 query sequences found.
[SEGEMEHL] Thu Aug 30 14:28:50 2018: reading database sequences.
[SEGEMEHL] Thu Aug 30 14:28:50 2018: 1 database sequences found.
[SEGEMEHL] Thu Aug 30 14:28:50 2018: total length of db sequences: 5132068
[SEGEMEHL] Thu Aug 30 14:28:50 2018: reading suffix array '/project/teaser/genometeaser/references/E_coli.fasta.idx' from disk.
[SEGEMEHL] Thu Aug 30 14:28:50 2018: reading lcpc/vtab.
[SEGEMEHL] Thu Aug 30 14:28:50 2018: reading childtab.
[SEGEMEHL] Thu Aug 30 14:28:50 2018: reading suflinks.
[SEGEMEHL] Thu Aug 30 14:28:50 2018: reading lsint id.
[SEGEMEHL] Thu Aug 30 14:28:50 2018: read suffix array '/project/teaser/genometeaser/references/E_coli.fasta.idx' with 5132069 elements.
[SEGEMEHL] Thu Aug 30 14:28:50 2018: md5 keys of index and db match.
[SEGEMEHL] Thu Aug 30 14:28:50 2018: reading the suffix array has taken 0.000000 seconds.
[= ] 0%(0) reads matched. /
[SEGEMEHL] Thu Aug 30 14:28:50 2018: matching w/ suffixarray has taken 0.000000 seconds.
[SEGEMEHL] Thu Aug 30 14:28:50 2018:
Goodbye.
"Mahlzeit!" (Ditsche, Ingo, Schildkroede)
systime0.184
time0.816411018372
usrtime0.344
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923

/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
memory90408000
return0
status1
stderr
None
stdout
[SEGEMEHL] Thu Aug 30 14:28:51 2018: reading queries in 'reads.fastq'.
[SEGEMEHL] Thu Aug 30 14:28:54 2018: 150000 query sequences found.
[SEGEMEHL] Thu Aug 30 14:28:54 2018: reading database sequences.
[SEGEMEHL] Thu Aug 30 14:28:54 2018: 1 database sequences found.
[SEGEMEHL] Thu Aug 30 14:28:54 2018: total length of db sequences: 5132068
[SEGEMEHL] Thu Aug 30 14:28:54 2018: reading suffix array '/project/teaser/genometeaser/references/E_coli.fasta.idx' from disk.
[SEGEMEHL] Thu Aug 30 14:28:54 2018: reading lcpc/vtab.
[SEGEMEHL] Thu Aug 30 14:28:55 2018: reading childtab.
[SEGEMEHL] Thu Aug 30 14:28:55 2018: reading suflinks.
[SEGEMEHL] Thu Aug 30 14:28:55 2018: reading lsint id.
[SEGEMEHL] Thu Aug 30 14:28:55 2018: read suffix array '/project/teaser/genometeaser/references/E_coli.fasta.idx' with 5132069 elements.
[SEGEMEHL] Thu Aug 30 14:28:55 2018: md5 keys of index and db match.
[SEGEMEHL] Thu Aug 30 14:28:55 2018: reading the suffix array has taken 1.000000 seconds.
[= ] 0%(0) reads matched. /
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[= ] 0%(90) reads matched. /
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[= ] 0%(150) reads matched. /
[= ] 0%(151) reads matched. /
systime16.192
time828.516000032
usrtime781.908
working_directory/project/teaser/genometeaser/tests_generated/3f0952a92d640dea6a7f5d449db65923