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 Mapped19703398.79%
Wrongly Mapped24131.21%
Not Mapped00.0%
Total199446100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome6420.322%
Mapped to wrong position17710.888%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.993900
Precision0.987900
Recall1.000000
Timing
Raw Mapping Time2293.688s
Effective Mapping Time2293.232s
Effective Init Time0.456s
Effective Time MeasureCPU
Mapping Time (Wall)559.123s
Mapping Time (CPU)2293.688s
Mapping Time (CPU User)2244.336s
Mapping Time (CPU System)49.352s
Init Time (Wall)0.621s
Init Time (CPU)0.456s
Init Time (CPU User)0.264s
Init Time (CPU System)0.192s
Additional Information
Mapper Memory Usage315 MB
Total Test Runtime (Wall)781.175s
Mapper Command Line: 
/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -h /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -o out_stampy.sam -M reads1.fastq reads2.fastq
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/stampy -G /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas; /project/teaser/genometeaser/software/stampy -g /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -H /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o

command/project/teaser/genometeaser/software/stampy -G /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas; /project/teaser/genometeaser/software/stampy -g /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -H /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o
return1
status1
stderr
None
stdout
stampy: Building genome...
stampy: Input files: ['/project/teaser/genometeaser/references/Arabidopsis_thaliana.fas']
stampy: Done
stampy: Building hash table...
stampy: Initializing...
stampy: Counting...
stampy: Working... (0.0 %) stampy: Working... (0.4 %) stampy: Working... (0.7 %) stampy: Working... (1.1 %) stampy: Working... (1.4 %) stampy: Working... (1.8 %) stampy: Working... (2.1 %) stampy: Working... (2.5 %) stampy: Working... (2.8 %) stampy: Working... (3.2 %) stampy: Working... (3.5 %) stampy: Working... (3.9 %) stampy: Working... (4.2 %) stampy: Working... (4.6 %) stampy: Working... (4.9 %) stampy: Working... (5.3 %) stampy: Working... (5.6 %) stampy: Working... (6.0 %) stampy: Working... (6.3 %) stampy: Working... (6.7 %) stampy: Working... (7.0 %) stampy: Working... (7.4 %) stampy: Working... (7.7 %) stampy: Working... (8.1 %) stampy: Working... (8.4 %) stampy: Working... (8.8 %) stampy: Working... (9.1 %) stampy: Working... (9.5 %) stampy: Working... (9.8 %) stampy: Working... (10.0 %) stampy: Working... (10.6 %) stampy: Working... (11.3 %) stampy: Working... (11.9 %) stampy: Working... (12.5 %) stampy: Working... (13.1 %) stampy: Working... (13.8 %) stampy: Working... (14.4 %) stampy: Working... (15.0 %) stampy: Working... (15.6 %) stampy: Working... (16.3 %) stampy: Working... (16.9 %) stampy: Working... (17.5 %) stampy: Working... (18.1 %) stampy: Working... (18.8 %) stampy: Working... (19.4 %) stampy: Initializing hash...
stampy: Flagging high counts...
stampy: Working... (20.0 %) stampy: Working... (20.6 %) stampy: Working... (21.3 %) stampy: Working... (21.9 %) stampy: Working... (22.5 %) stampy: Working... (23.1 %) stampy: Working... (23.8 %) stampy: Working... (24.4 %) stampy: Working... (25.0 %) stampy: Working... (25.6 %) stampy: Working... (26.3 %) stampy: Working... (26.9 %) stampy: Working... (27.5 %) stampy: Working... (28.1 %) stampy: Working... (28.8 %) stampy: Working... (29.4 %) stampy: Creating hash...
stampy: Working... (27.3 %) stampy: Working... (28.9 %) stampy: Working... (30.5 %) stampy: Working... (32.1 %) stampy: Working... (33.6 %) stampy: Working... (35.2 %) stampy: Working... (36.4 %) stampy: Working... (38.0 %) stampy: Working... (39.5 %) stampy: Working... (41.1 %) stampy: Working... (42.7 %) stampy: Working... (44.3 %) stampy: Working... (45.5 %) stampy: Working... (47.0 %) stampy: Working... (48.6 %) stampy: Working... (50.2 %) stampy: Working... (51.8 %) stampy: Working... (53.4 %) stampy: Working... (54.5 %) stampy: Working... (56.1 %) stampy: Working... (57.7 %) stampy: Working... (59.3 %) stampy: Working... (60.9 %) stampy: Working... (62.5 %) stampy: Working... (63.6 %) stampy: Working... (65.2 %) stampy: Working... (66.8 %) stampy: Working... (68.4 %) stampy: Working... (70.0 %) stampy: Working... (71.6 %) stampy: Working... (72.7 %) stampy: Working... (74.3 %) stampy: Working... (75.9 %) stampy: Working... (77.5 %) stampy: Working... (79.1 %) stampy: Working... (80.7 %) stampy: Working... (81.8 %) stampy: Working... (83.4 %) stampy: Working... (85.0 %) stampy: Working... (86.6 %) stampy: Working... (88.2 %) stampy: Working... (89.8 %) stampy: Working... (90.9 %) stampy: Working... (92.5 %) stampy: Working... (94.1 %) stampy: Working... (95.7 %) stampy: Working... (97.3 %) stampy: Working... (98.9 %) stampy: Writing...
stampy: Finished building hash table
stampy: Done
systime0
time167.98687005
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679

/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -h /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -M reads_base.fastq -o out_stampy.sam

command/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -h /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -M reads_base.fastq -o out_stampy.sam
memory307152000
return0
status1
stderr
None
stdout
stampy: Mapping...
stampy: # Nucleotides (all/1/2): 0 0 0
stampy: # Variants: 0 0 0
stampy: # Fraction: 0.0000 0.0000 0.0000
stampy: Done
systime0.34
time3.64621305466
usrtime0.452
working_directory/project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679

/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -h /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -M reads_base.fastq -o out_stampy.sam

command/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -h /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -M reads_base.fastq -o out_stampy.sam
memory306296000
return1
status1
stderr
None
stdout

stampy: Error: File out_stampy.sam exists
systime0.192
time0.620845794678
usrtime0.264
working_directory/project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679

/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -h /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -o out_stampy.sam -M reads1.fastq reads2.fastq

command/project/teaser/genometeaser/software/stampy -t 4 -g /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -h /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_o -o out_stampy.sam -M reads1.fastq reads2.fastq
memory315276000
return0
status1
stderr
None
stdout
stampy: Mapping...
stampy: # Nucleotides (all/1/2): 29916900 14958450 14958450
stampy: # Variants: 1018912 509473 509439
stampy: # Fraction: 0.0341 0.0341 0.0341
stampy: # Paired-end insert size: 329.4 +/- 105.5 (99501 pairs)
stampy: Done
systime49.352
time559.122933149
usrtime2244.336
working_directory/project/teaser/genometeaser/tests_generated/ff62cbf4348f21949b4a4be50bea9679