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 Mapped48541897.353%
Wrongly Mapped131952.646%
Not Mapped10.0%
Total498614100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output10.0%
Mapped to wrong chromosome49020.983%
Mapped to wrong position82931.663%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.986600
Precision0.973500
Recall1.000000
Timing
Raw Mapping Time479.788s
Effective Mapping Time470.892s
Effective Init Time8.896s
Effective Time MeasureCPU
Mapping Time (Wall)480.500s
Mapping Time (CPU)479.788s
Mapping Time (CPU User)463.652s
Mapping Time (CPU System)16.136s
Init Time (Wall)9.034s
Init Time (CPU)8.896s
Init Time (CPU User)6.820s
Init Time (CPU System)2.076s
Additional Information
Mapper Memory Usage1897 MB
Total Test Runtime (Wall)706.490s
Mapper Command Line: 
/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.idx -d /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas -q reads1.fastq -p reads2.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/Arabidopsis_thaliana.fas.idx -d /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas -q reads_base.fastq > out_segemehl.sam

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.idx -d /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas -q reads_base.fastq > out_segemehl.sam
memory1896584000
return0
status1
stderr
None
stdout
[SEGEMEHL] Tue Oct 16 14:42:59 2018: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Tue Oct 16 14:42:59 2018: 1 query sequences found.
[SEGEMEHL] Tue Oct 16 14:42:59 2018: reading database sequences.
[SEGEMEHL] Tue Oct 16 14:43:09 2018: 7 database sequences found.
[SEGEMEHL] Tue Oct 16 14:43:09 2018: total length of db sequences: 119667750
[SEGEMEHL] Tue Oct 16 14:43:09 2018: reading suffix array '/project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.idx' from disk.
[SEGEMEHL] Tue Oct 16 14:43:51 2018: reading lcpc/vtab.
[SEGEMEHL] Tue Oct 16 14:44:02 2018: reading childtab.
[SEGEMEHL] Tue Oct 16 14:44:42 2018: reading suflinks.
[SEGEMEHL] Tue Oct 16 14:45:33 2018: reading lsint id.
[SEGEMEHL] Tue Oct 16 14:45:34 2018: read suffix array '/project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.idx' with 119667757 elements.
[SEGEMEHL] Tue Oct 16 14:45:35 2018: md5 keys of index and db match.
[SEGEMEHL] Tue Oct 16 14:45:35 2018: reading the suffix array has taken 146.000000 seconds.
[= ] 0%(0) reads matched. /
[SEGEMEHL] Tue Oct 16 14:45:35 2018: matching w/ suffixarray has taken 0.000000 seconds.
[SEGEMEHL] Tue Oct 16 14:45:35 2018:
Goodbye.
"Wir sind hier nicht in Seattle Dirk!" (Tocotronic)
systime2.708
time156.261427879
usrtime6.84
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af

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

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.idx -d /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas -q reads_base.fastq > out_segemehl.sam
memory1895840000
return0
status1
stderr
None
stdout
[SEGEMEHL] Tue Oct 16 14:45:36 2018: reading queries in 'reads_base.fastq'.
[SEGEMEHL] Tue Oct 16 14:45:36 2018: 1 query sequences found.
[SEGEMEHL] Tue Oct 16 14:45:36 2018: reading database sequences.
[SEGEMEHL] Tue Oct 16 14:45:42 2018: 7 database sequences found.
[SEGEMEHL] Tue Oct 16 14:45:42 2018: total length of db sequences: 119667750
[SEGEMEHL] Tue Oct 16 14:45:42 2018: reading suffix array '/project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.idx' from disk.
[SEGEMEHL] Tue Oct 16 14:45:43 2018: reading lcpc/vtab.
[SEGEMEHL] Tue Oct 16 14:45:43 2018: reading childtab.
[SEGEMEHL] Tue Oct 16 14:45:44 2018: reading suflinks.
[SEGEMEHL] Tue Oct 16 14:45:44 2018: reading lsint id.
[SEGEMEHL] Tue Oct 16 14:45:44 2018: read suffix array '/project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.idx' with 119667757 elements.
[SEGEMEHL] Tue Oct 16 14:45:45 2018: md5 keys of index and db match.
[SEGEMEHL] Tue Oct 16 14:45:45 2018: reading the suffix array has taken 3.000000 seconds.
[= ] 0%(0) reads matched. /
[SEGEMEHL] Tue Oct 16 14:45:45 2018: matching w/ suffixarray has taken 0.000000 seconds.
[SEGEMEHL] Tue Oct 16 14:45:45 2018:
Goodbye.
"Ich bin neu in der Hamburger Schule" (Tocotronic)
systime2.076
time9.03401708603
usrtime6.82
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af

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

command/project/teaser/genometeaser/software/segemehl.x -r 1 -i /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.idx -d /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas -q reads1.fastq -p reads2.fastq > out_segemehl.sam
memory1897660000
return0
status1
stderr
None
stdout
[SEGEMEHL] Tue Oct 16 14:45:46 2018: reading queries in 'reads1.fastq'.
[SEGEMEHL] Tue Oct 16 14:45:48 2018: 249307 query sequences found.
[SEGEMEHL] Tue Oct 16 14:45:48 2018: reading mates in 'reads2.fastq'.
[SEGEMEHL] Tue Oct 16 14:45:50 2018: 249307 mate sequences found.
[SEGEMEHL] Tue Oct 16 14:45:50 2018: reading database sequences.
[SEGEMEHL] Tue Oct 16 14:45:56 2018: 7 database sequences found.
[SEGEMEHL] Tue Oct 16 14:45:56 2018: total length of db sequences: 119667750
[SEGEMEHL] Tue Oct 16 14:45:56 2018: reading suffix array '/project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.idx' from disk.
[SEGEMEHL] Tue Oct 16 14:45:57 2018: reading lcpc/vtab.
[SEGEMEHL] Tue Oct 16 14:45:58 2018: reading childtab.
[SEGEMEHL] Tue Oct 16 14:45:58 2018: reading suflinks.
[SEGEMEHL] Tue Oct 16 14:45:58 2018: reading lsint id.
[SEGEMEHL] Tue Oct 16 14:45:58 2018: read suffix array '/project/teaser/genometeaser/references/Arabidopsis_thaliana.fas.idx' with 119667757 elements.
[SEGEMEHL] Tue Oct 16 14:45:59 2018: md5 keys of index and db match.
[SEGEMEHL] Tue Oct 16 14:45:59 2018: reading the suffix array has taken 3.000000 seconds.
[= ] 0%(0) reads matched. /
[= ] 0%(1) reads matched. /
[= ] 0%(2) reads matched. /
[= ] 0%(3) reads matched. /
[= ] 0%(4) reads matched. /
[= ] 0%(5) reads matched. /
[= ] 0%(6) reads matched. /
[= ] 0%(7) reads matched. /
[= ] 0%(8) reads matched. /
[= ] 0%(9) reads matched. /
[= ] 0%(10) reads matched. /
[= ] 0%(11) reads matched. \
[= ] 0%(12) reads matched. \
[= ] 0%(13) reads matched. \
[= ] 0%(14) reads matched. \
[= ] 0%(15) reads matched. \
[= ] 0%(16) reads matched. \
[= ] 0%(17) reads matched. \
[= ] 0%(18) reads matched. \
[= ] 0%(19) reads matched. \
[= ] 0%(20) reads matched. \
[= ] 0%(21) reads matched. -
[= ] 0%(22) reads matched. -
[= ] 0%(23) reads matched. -
[= ] 0%(24) reads matched. -
[= ] 0%(25) reads matched. -
[= ] 0%(26) reads matched. -
[= ] 0%(27) reads matched. -
[= ] 0%(28) reads matched. -
[= ] 0%(29) reads matched. -
[= ] 0%(30) reads matched. /
[= ] 0%(31) reads matched. /
[= ] 0%(32) reads matched. /
[= ] 0%(33) reads matched. /
[= ] 0%(34) reads matched. /
[= ] 0%(35) reads matched. /
[= ] 0%(36) reads matched. /
[= ] 0%(37) reads matched. /
[= ] 0%(38) reads matched. /
[= ] 0%(39) reads matched. /
[= ] 0%(40) reads matched. /
[= ] 0%(41) reads matched. \
[= ] 0%(42) reads matched. \
[= ] 0%(43) reads matched. \
[= ] 0%(44) reads matched. \
[= ] 0%(45) reads matched. \
[= ] 0%(46) reads matched. \
[= ] 0%(47) reads matched. \
[= ] 0%(48) reads matched. \
[= ] 0%(49) reads matched. \
[= ] 0%(50) reads matched. \
[= ] 0%(51) reads matched. -
[= ] 0%(52) reads matched. -
[= ] 0%(53) reads matched. -
[= ] 0%(54) reads matched. -
[= ] 0%(55) reads matched. -
[= ] 0%(56) reads matched. -
[= ] 0%(57) reads matched. -
[= ] 0%(58) reads matched. -
[= ] 0%(59) reads matched. -
[= ] 0%(60) reads matched. /
[= ] 0%(61) reads matched. /
[= ] 0%(62) reads matched. /
[= ] 0%(63) reads matched. /
[= ] 0%(64) reads matched. /
[= ] 0%(65) reads matched. /
[= ] 0%(66) reads matched. /
[= ] 0%(67) reads matched. /
[= ] 0%(68) reads matched. /
[= ] 0%(69) reads matched. /
[= ] 0%(70) reads matched. /
[= ] 0%(71) reads matched. \
[= ] 0%(72) reads matched. \
[= ] 0%(73) reads matched. \
[= ] 0%(74) reads matched. \
[= ] 0%(75) reads matched. \
[= ] 0%(76) reads matched. \
[= ] 0%(77) reads matched. \
[= ] 0%(78) reads matched. \
[= ] 0%(79) reads matched. \
[= ] 0%(80) reads matched. \
[= ] 0%(81) reads matched. -
[= ] 0%(82) reads matched. -
[= ] 0%(83) reads matched. -
[= ] 0%(84) reads matched. -
[= ] 0%(85) reads matched. -
[= ] 0%(86) reads matched. -
[= ] 0%(87) reads matched. -
[= ] 0%(88) reads matched. -
[= ] 0%(89) reads matched. -
[= ] 0%(90) reads matched. /
[= ] 0%(91) reads matched. /
[= ] 0%(92) reads matched. /
[= ] 0%(93) reads matched. /
[= ] 0%(94) reads matched. /
[= ] 0%(95) reads matched. /
[= ] 0%(96) reads matched. /
[= ] 0%(97) reads matched. /
[= ] 0%(98) reads matched. /
[= ] 0%(99) reads matched. /
[= ] 0%(100) reads matched. /
[= ] 0%(101) reads matched. \
[= ] 0%(102) reads matched. \
[= ] 0%(103) reads matched. \
[= ] 0%(104) reads matched. \
[= ] 0%(105) reads matched. \
[= ] 0%(106) reads matched. \
[= ] 0%(107) reads matched. \
[= ] 0%(108) reads matched. \
[= ] 0%(109) reads matched. \
[= ] 0%(110) reads matched. \
[= ] 0%(111) reads matched. -
[= ] 0%(112) reads matched. -
[= ] 0%(113) reads matched. -
[= ] 0%(114) reads matched. -
[= ] 0%(115) reads matched. -
[= ] 0%(116) reads matched. -
[= ] 0%(117) reads matched. -
[= ] 0%(118) reads matched. -
[= ] 0%(119) reads matched. -
[= ] 0%(120) reads matched. /
[= ] 0%(121) reads matched. /
[= ] 0%(122) reads matched. /
[= ] 0%(123) reads matched. /
[= ] 0%(124) reads matched. /
[= ] 0%(125) reads matched. /
[= ] 0%(126) reads matched. /
[= ] 0%(127) reads matched. /
[= ] 0%(128) reads matched. /
[= ] 0%(129) reads matched. /
[= ] 0%(130) reads matched. /
[= ] 0%(131) reads matched. \
[= ] 0%(132) reads matched. \
[= ] 0%(133) reads matched. \
[= ] 0%(134) reads matched. \
[= ] 0%(135) reads matched. \
[= ] 0%(136) reads matched. \
[= ] 0%(137) reads matched. \
[= ] 0%(138) reads matched. \
[= ] 0%(139) reads matched. \
[= ] 0%(140) reads matched. \
[= ] 0%(141) reads matched. -
[= ] 0%(142) reads matched. -
[= ] 0%(143) reads matched. -
[= ] 0%(144) reads matched. -
[= ] 0%(145) reads matched. -
[= ] 0%(146) reads matched. -
[= ] 0%(147) reads matched. -
[= ] 0%(148) reads matched. -
[=
systime16.136
time480.500174999
usrtime463.652
working_directory/project/teaser/genometeaser/tests_generated/340a758089e3620a129e06c436f2f4af