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 Mapped209144100.0%
Total209144100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output209144100.0%
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 Time176.964s
Effective Mapping Time3.764s
Effective Init Time173.200s
Effective Time MeasureCPU
Mapping Time (Wall)177.068s
Mapping Time (CPU)176.964s
Mapping Time (CPU User)170.140s
Mapping Time (CPU System)6.824s
Init Time (Wall)173.259s
Init Time (CPU)173.200s
Init Time (CPU User)166.080s
Init Time (CPU System)7.120s
Additional Information
Mapper Memory Usage6131 MB
Total Test Runtime (Wall)652.909s
Mapper Command Line: 
/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/H_sapiens.fa.idx -d /project/teaser/genometeaser/references/H_sapiens.fa -q reads1.fastq -p reads2.fastq > out_segemehl.sam
Errors and Warnings
TypeMessageFilePosition
Unexpectedly reached end of mapper outputsorted_out_segemehl.samread.000000000
Subprocess Log

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

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/H_sapiens.fa.idx -d /project/teaser/genometeaser/references/H_sapiens.fa -q reads_base.fastq > out_segemehl.sam
memory6131116000
return134
status1
stderr
None
stdout
[SEGEMEHL] Fri Jul 13 18:19:42 2018: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Fri Jul 13 18:19:42 2018: 1 query sequences found.
[SEGEMEHL] Fri Jul 13 18:19:42 2018: reading database sequences.
[SEGEMEHL] Fri Jul 13 18:24:14 2018: 93 database sequences found.
[SEGEMEHL] Fri Jul 13 18:24:14 2018: total length of db sequences: 3137161264
[SEGEMEHL] Fri Jul 13 18:24:14 2018: reading suffix array '/project/teaser/genometeaser/references/H_sapiens.fa.idx' from disk.
segemehl.x: libs/memory.c:18: bl_realloc: Assertion `ptr != ((void *)0)' failed.
/bin/sh: line 1: 64159 Aborted /project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/H_sapiens.fa.idx -d /project/teaser/genometeaser/references/H_sapiens.fa -q reads_base.fastq > out_segemehl.sam
systime7.568
time288.322075129
usrtime165.828
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

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

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/H_sapiens.fa.idx -d /project/teaser/genometeaser/references/H_sapiens.fa -q reads_base.fastq > out_segemehl.sam
memory6131200000
return134
status1
stderr
None
stdout
[SEGEMEHL] Fri Jul 13 18:24:32 2018: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Fri Jul 13 18:24:32 2018: 1 query sequences found.
[SEGEMEHL] Fri Jul 13 18:24:32 2018: reading database sequences.
[SEGEMEHL] Fri Jul 13 18:27:08 2018: 93 database sequences found.
[SEGEMEHL] Fri Jul 13 18:27:08 2018: total length of db sequences: 3137161264
[SEGEMEHL] Fri Jul 13 18:27:08 2018: reading suffix array '/project/teaser/genometeaser/references/H_sapiens.fa.idx' from disk.
segemehl.x: libs/memory.c:18: bl_realloc: Assertion `ptr != ((void *)0)' failed.
/bin/sh: line 1: 64186 Aborted /project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/H_sapiens.fa.idx -d /project/teaser/genometeaser/references/H_sapiens.fa -q reads_base.fastq > out_segemehl.sam
systime7.12
time173.258766174
usrtime166.08
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

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

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/H_sapiens.fa.idx -d /project/teaser/genometeaser/references/H_sapiens.fa -q reads1.fastq -p reads2.fastq > out_segemehl.sam
memory6131212000
return134
status1
stderr
None
stdout
[SEGEMEHL] Fri Jul 13 18:27:26 2018: reading queries in 'reads1.fastq'.
[SEGEMEHL] Fri Jul 13 18:27:28 2018: 104572 query sequences found.
[SEGEMEHL] Fri Jul 13 18:27:28 2018: reading mates in 'reads2.fastq'.
[SEGEMEHL] Fri Jul 13 18:27:29 2018: 104572 mate sequences found.
[SEGEMEHL] Fri Jul 13 18:27:29 2018: reading database sequences.
[SEGEMEHL] Fri Jul 13 18:30:06 2018: 93 database sequences found.
[SEGEMEHL] Fri Jul 13 18:30:06 2018: total length of db sequences: 3137161264
[SEGEMEHL] Fri Jul 13 18:30:06 2018: reading suffix array '/project/teaser/genometeaser/references/H_sapiens.fa.idx' from disk.
segemehl.x: libs/memory.c:18: bl_realloc: Assertion `ptr != ((void *)0)' failed.
/bin/sh: line 1: 64204 Aborted /project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/H_sapiens.fa.idx -d /project/teaser/genometeaser/references/H_sapiens.fa -q reads1.fastq -p reads2.fastq > out_segemehl.sam
systime6.824
time177.06754899
usrtime170.14
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12