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 Mapped313713100.0%
Total313713100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output313713100.0%
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 Time63.269s
Effective Mapping Time1.135s
Effective Init Time62.135s
Effective Time MeasureCPU
Mapping Time (Wall)63.517s
Mapping Time (CPU)63.269s
Mapping Time (CPU User)60.490s
Mapping Time (CPU System)2.780s
Init Time (Wall)62.331s
Init Time (CPU)62.135s
Init Time (CPU User)59.412s
Init Time (CPU System)2.723s
Additional Information
Mapper Memory Usage6128 MB
Total Test Runtime (Wall)563.368s
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.samY29udGlnXzc0MDA4OTJfNzQwMDk3Ml8wXzFfMF8wXzI6MDowXzA6MDowXzczMmQ=
Subprocess Log

/project/teaser/genometeaser/software/segemehl.x -x /project/teaser/genometeaser/references/H_sapiens.fa.idx -d /project/teaser/genometeaser/references/H_sapiens.fa

command/project/teaser/genometeaser/software/segemehl.x -x /project/teaser/genometeaser/references/H_sapiens.fa.idx -d /project/teaser/genometeaser/references/H_sapiens.fa
return1
status1
stderr
None
stdout
[SEGEMEHL] Thu May 11 03:46:05 2017: reading database sequences.
[SEGEMEHL] Thu May 11 03:47:03 2017: 93 database sequences found.
[SEGEMEHL] Thu May 11 03:47:03 2017: total length of db sequences: 3137161264
[SEGEMEHL] Thu May 11 03:47:19 2017: alphabet of size (7): ACGNT~
[SEGEMEHL] Thu May 11 03:47:19 2017: size of db sequence: 3137161357
[SEGEMEHL] Thu May 11 03:47:19 2017: constructing suftab.
[SEGEMEHL] Thu May 11 03:47:19 2017: alurusort: classify
init bit array of 392145170
[SEGEMEHL] Thu May 11 03:47:46 2017: alurusort: getting bit
[SEGEMEHL] Thu May 11 03:47:46 2017: not bit alurusort: alloc B of size 1381049490
[SEGEMEHL] Thu May 11 03:47:46 2017: alurusort: initbitarray of size 1381049490
init bit array of 172631187
[SEGEMEHL] Thu May 11 03:47:46 2017: alurusort: Qmaxdist in cl of size 3137161357
[SEGEMEHL] Thu May 11 03:47:55 2017: alurusort: scan B
[SEGEMEHL] Thu May 11 03:48:05 2017: alurusort: substringsort
[SEGEMEHL] Thu May 11 03:48:05 2017: setting bit array to zero
[SEGEMEHL] Thu May 11 03:48:06 2017: allocating space for buckets and buffers
[SEGEMEHL] Thu May 11 03:48:06 2017: memsetting
[SEGEMEHL] Thu May 11 03:52:06 2017: substring sort ... ok
[SEGEMEHL] Thu May 11 03:52:07 2017: checking valbitarray
[SEGEMEHL] Thu May 11 03:52:07 2017: enter Tprime calculation[SEGEMEHL] Thu May 11 03:52:07 2017: tprime: init arrays
segemehl.x: libs/memory.c:18: bl_realloc: Assertion `ptr != ((void *)0)' failed.
systime0
time362.986842155
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3

/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
memory6128676000
return255
status1
stderr
None
stdout
[SEGEMEHL] Thu May 11 03:52:09 2017: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Thu May 11 03:52:09 2017: 1 query sequences found.
[SEGEMEHL] Thu May 11 03:52:09 2017: reading database sequences.
[SEGEMEHL] Thu May 11 03:53:07 2017: 93 database sequences found.
[SEGEMEHL] Thu May 11 03:53:07 2017: total length of db sequences: 3137161264
[SEGEMEHL] Thu May 11 03:53:07 2017: reading suffix array '/project/teaser/genometeaser/references/H_sapiens.fa.idx' from disk.
[SEGEMEHL] file: libs/sufarray/sufarray.c, line: 325: Couldn't open file '/project/teaser/genometeaser/references/H_sapiens.fa.idx'. Exit forced.
systime3.884409
time67.2584559917
usrtime62.939431
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3

/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
memory6128676000
return255
status1
stderr
None
stdout
[SEGEMEHL] Thu May 11 03:53:17 2017: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Thu May 11 03:53:17 2017: 1 query sequences found.
[SEGEMEHL] Thu May 11 03:53:17 2017: reading database sequences.
[SEGEMEHL] Thu May 11 03:54:10 2017: 93 database sequences found.
[SEGEMEHL] Thu May 11 03:54:10 2017: total length of db sequences: 3137161264
[SEGEMEHL] Thu May 11 03:54:10 2017: reading suffix array '/project/teaser/genometeaser/references/H_sapiens.fa.idx' from disk.
[SEGEMEHL] file: libs/sufarray/sufarray.c, line: 325: Couldn't open file '/project/teaser/genometeaser/references/H_sapiens.fa.idx'. Exit forced.
systime2.722586
time62.3312950134
usrtime59.411968
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3

/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
memory6128696000
return255
status1
stderr
None
stdout
[SEGEMEHL] Thu May 11 03:54:20 2017: reading queries in 'reads1.fastq'.
[SEGEMEHL] Thu May 11 03:54:21 2017: 156858 query sequences found.
[SEGEMEHL] Thu May 11 03:54:21 2017: reading mates in 'reads2.fastq'.
[SEGEMEHL] Thu May 11 03:54:22 2017: 156858 mate sequences found.
[SEGEMEHL] Thu May 11 03:54:22 2017: reading database sequences.
[SEGEMEHL] Thu May 11 03:55:15 2017: 93 database sequences found.
[SEGEMEHL] Thu May 11 03:55:15 2017: total length of db sequences: 3137161264
[SEGEMEHL] Thu May 11 03:55:15 2017: reading suffix array '/project/teaser/genometeaser/references/H_sapiens.fa.idx' from disk.
[SEGEMEHL] file: libs/sufarray/sufarray.c, line: 325: Couldn't open file '/project/teaser/genometeaser/references/H_sapiens.fa.idx'. Exit forced.
systime2.779577
time63.5174269676
usrtime60.489804
working_directory/project/teaser/genometeaser/tests_generated/cc90747119948fac5bcca0e53c33f3a3