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 Mapped418288100.0%
Total418288100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output418288100.0%
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 Time275.208s
Effective Mapping Time77.624s
Effective Init Time197.584s
Effective Time MeasureCPU
Mapping Time (Wall)276.397s
Mapping Time (CPU)275.208s
Mapping Time (CPU User)163.812s
Mapping Time (CPU System)111.396s
Init Time (Wall)198.811s
Init Time (CPU)197.584s
Init Time (CPU User)84.764s
Init Time (CPU System)112.820s
Additional Information
Mapper Memory Usage6131 MB
Total Test Runtime (Wall)843.848s
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
memory6131084000
return134
status1
stderr
None
stdout
[SEGEMEHL] Sat Sep  9 17:57:43 2017: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Sat Sep 9 17:57:43 2017: 1 query sequences found.
[SEGEMEHL] Sat Sep 9 17:57:43 2017: reading database sequences.
[SEGEMEHL] Sat Sep 9 18:02:16 2017: 93 database sequences found.
[SEGEMEHL] Sat Sep 9 18:02:16 2017: total length of db sequences: 3137161264
[SEGEMEHL] Sat Sep 9 18:02:16 2017: 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: 25443 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
systime112.636
time345.776295185
usrtime158.976
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1

/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
memory6131236000
return134
status1
stderr
None
stdout
[SEGEMEHL] Sat Sep  9 18:03:30 2017: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Sat Sep 9 18:03:30 2017: 1 query sequences found.
[SEGEMEHL] Sat Sep 9 18:03:30 2017: reading database sequences.
[SEGEMEHL] Sat Sep 9 18:05:41 2017: 93 database sequences found.
[SEGEMEHL] Sat Sep 9 18:05:41 2017: total length of db sequences: 3137161264
[SEGEMEHL] Sat Sep 9 18:05:41 2017: 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: 30971 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
systime112.82
time198.811036825
usrtime84.764
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1

/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
memory6131104000
return134
status1
stderr
None
stdout
[SEGEMEHL] Sat Sep  9 18:06:49 2017: reading queries in 'reads1.fastq'.
[SEGEMEHL] Sat Sep 9 18:06:51 2017: 209144 query sequences found.
[SEGEMEHL] Sat Sep 9 18:06:51 2017: reading mates in 'reads2.fastq'.
[SEGEMEHL] Sat Sep 9 18:06:53 2017: 209144 mate sequences found.
[SEGEMEHL] Sat Sep 9 18:06:53 2017: reading database sequences.
[SEGEMEHL] Sat Sep 9 18:10:13 2017: 93 database sequences found.
[SEGEMEHL] Sat Sep 9 18:10:13 2017: total length of db sequences: 3137161264
[SEGEMEHL] Sat Sep 9 18:10:13 2017: 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: 34054 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
systime111.396
time276.396700859
usrtime163.812
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1