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 Mapped14728298.188%
Wrongly Mapped27081.805%
Not Mapped100.007%
Total150000100.0%
Read Failure Statistics
Not mapped100.007%
Missing in mapper output00.0%
Mapped to wrong chromosome22011.467%
Mapped to wrong position5070.338%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.990900
Precision0.981900
Recall0.999900
Timing
Raw Mapping Time41.513s
Effective Mapping Time41.272s
Effective Init Time0.241s
Effective Time MeasureCPU
Mapping Time (Wall)11.080s
Mapping Time (CPU)41.513s
Mapping Time (CPU User)41.121s
Mapping Time (CPU System)0.392s
Init Time (Wall)0.218s
Init Time (CPU)0.241s
Init Time (CPU User)0.053s
Init Time (CPU System)0.188s
Additional Information
Mapper Memory Usage104 MB
Total Test Runtime (Wall)46.863s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bowtie2/bowtie2-build /project/teaser/genometeaser/references/Cryptosporidium.fasta /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt

command/project/teaser/genometeaser/software/bowtie2/bowtie2-build /project/teaser/genometeaser/references/Cryptosporidium.fasta /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt
return1
status1
stderr
None
stdout
Settings:
Output files: "/project/teaser/genometeaser/references/Cryptosporidium.fasta_bt.*.bt2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
/project/teaser/genometeaser/references/Cryptosporidium.fasta
Building a SMALL index
Reading reference sizes
Time reading reference sizes: 00:00:01
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 4729601
Using parameters --bmax 3547201 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 3547201 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:00
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:01
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:00
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Binary sorting into buckets
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Binary sorting into buckets time: 00:00:01
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 5; iterating...
Binary sorting into buckets
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Binary sorting into buckets time: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 2.70263e+06 (target: 3547200)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 3079427
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Sorting block time: 00:00:00
Returning block of 3079428
Getting block 2 of 7
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 3534880
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 3534881
Getting block 3 of 7
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 3353933
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 3353934
Getting block 4 of 7
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 1907632
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 1907633
Getting block 5 of 7
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 2341530
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 2341531
Getting block 6 of 7
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:01
Sorting block of length 3495403
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Sorting block time: 00:00:01
Returning block of 3495404
Getting block 7 of 7
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 1205596
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 1205597
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 4898128
fchr[G]: 9459873
fchr[T]: 14019098
fchr[$]: 18918407
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 10501910 bytes to primary EBWT file: /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt.1.bt2
Wrote 4729608 bytes to secondary EBWT file: /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 18918407
bwtLen: 18918408
sz: 4729602
bwtSz: 4729602
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 1182401
offsSz: 4729604
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 98534
numLines: 98534
ebwtTotLen: 6306176
ebwtTotSz: 6306176
color: 0
reverse: 0
Total time for call to driver() for forward index: 00:00:12
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 4729601
Using parameters --bmax 3547201 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 3547201 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:00
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:00
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:01
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Binary sorting into buckets
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Binary sorting into buckets time: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
Binary sorting into buckets
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Binary sorting into buckets time: 00:00:01
Splitting and merging
Splitting and merging time: 00:00:00
Split 2, merged 1; iterating...
Binary sorting into buckets
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Binary sorting into buckets time: 00:00:01
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
Binary sorting into buckets
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Binary sorting into buckets time: 00:00:01
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 2.3648e+06 (target: 3547200)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 2519002
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 2519003
Getting block 2 of 8
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 2399000
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 2399001
Getting block 3 of 8
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 2055396
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 2055397
Getting block 4 of 8
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 1790175
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 1790176
Getting block 5 of 8
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 2896705
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 2896706
Getting block 6 of 8
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 2171691
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 2171692
Getting block 7 of 8
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 2583483
(Using difference cover)
Sorting block time: 00:00:01
Returning block of 2583484
Getting block 8 of 8
Reserving size (3547201) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:00
Sorting block of length 2502948
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Sorting block time: 00:00:01
Returning block of 2502949
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 4898128
fchr[G]: 9459873
fchr[T]: 14019098
fchr[$]: 18918407
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 10501910 bytes to primary EBWT file: /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt.rev.1.bt2
Wrote 4729608 bytes to secondary EBWT file: /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 18918407
bwtLen: 18918408
sz: 4729602
bwtSz: 4729602
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 1182401
offsSz: 4729604
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 98534
numLines: 98534
ebwtTotLen: 6306176
ebwtTotSz: 6306176
color: 0
reverse: 1
Total time for backward call to driver() for mirror index: 00:00:12
systime0
time24.1106209755
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory66480000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime0.197969
time0.271405220032
usrtime0.056991
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory69880000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime0.187971
time0.217693090439
usrtime0.052991
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Cryptosporidium.fasta_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory104184000
return0
status1
stderr
None
stdout
75000 reads; of these:
75000 (100.00%) were paired; of these:
37125 (49.50%) aligned concordantly 0 times
36018 (48.02%) aligned concordantly exactly 1 time
1857 (2.48%) aligned concordantly >1 times
----
37125 pairs aligned concordantly 0 times; of these:
35139 (94.65%) aligned discordantly 1 time
----
1986 pairs aligned 0 times concordantly or discordantly; of these:
3972 mates make up the pairs; of these:
10 (0.25%) aligned 0 times
138 (3.47%) aligned exactly 1 time
3824 (96.27%) aligned >1 times
99.99% overall alignment rate
systime0.39194
time11.0802869797
usrtime41.120748
working_directory/project/teaser/genometeaser/tests_generated/f23fe16b99420742b88a981972af6aae