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 Mapped20351897.31%
Wrongly Mapped54862.623%
Not Mapped1400.067%
Total209144100.0%
Read Failure Statistics
Not mapped1400.067%
Missing in mapper output00.0%
Mapped to wrong chromosome36631.751%
Mapped to wrong position18230.872%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.986400
Precision0.973800
Recall0.999300
Timing
Raw Mapping Time109.536s
Effective Mapping Time102.192s
Effective Init Time7.344s
Effective Time MeasureCPU
Mapping Time (Wall)43.082s
Mapping Time (CPU)109.536s
Mapping Time (CPU User)100.636s
Mapping Time (CPU System)8.900s
Init Time (Wall)7.110s
Init Time (CPU)7.344s
Init Time (CPU User)2.236s
Init Time (CPU System)5.108s
Additional Information
Mapper Memory Usage6657 MB
Total Test Runtime (Wall)94.052s
Mapper Command Line: 
/software/ngm/bin-linux/ngm-0.4.11 --qry2 reads2.fastq --output out_ngm_0_4_11.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --no-progress
Errors and Warnings
No problems were encountered.
Subprocess Log

/software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq --no-progress
memory5586816000
return0
status1
stderr
None
stdout
No protocol specified
[MAIN] NextGenMap 0.4.11
[MAIN] Startup : x64 (build Apr 19 2014 08:01:02)
[MAIN] Starting time: 2018-07-13.18:18:08
[CONFIG] Parameter: --affine 0 --block_multiplier 2 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 4 --dualstrand 1 --fast_pairing 0 --format 1 --gap_extend_penalty 5 --gap_read_penalty 20 --gap_ref_penalty 20 --hard_clip 0 --keep_tags 0 --kmer 13 --kmer_min 0 --kmer_skip 2 --match_bonus 10 --match_bonus_tc 4 --match_bonus_tt 4 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --min_identity 0.650000 --min_insert_size 0 --min_mq 0 --min_residues 0.500000 --min_score 0.000000 --mismatch_penalty 15 --mode 0 --no_progress 1 --no_unal 0 --ocl_threads 1 --output out_ngm_0_4_11.sam --overwrite 1 --pair_score_cutoff 0.900000 --paired 0 --parse_all 1 --pe_delimiter / --qry reads_base.fastq --qry_count -1 --qry_start 0 --ref /project/teaser/genometeaser/references/H_sapiens.fa --ref_mode -1 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --step_count 4 --strata 0 --topn 1
[STATS] Exporting stats at 0x33e32000 (Key 0x7328763d, ID 0x3b8001)
[NGM] Opening for output (SAM): out_ngm_0_4_11.sam
[NGM] NGM Core initialization
[SEQPROV] Init sequence provider.
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/H_sapiens.fa-enc.ngm
[SEQPROV] Reading from disk took 1.20s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/H_sapiens.fa-ht-13-2.ngm
[PREPROCESS] Reading from disk took 3.57s
[INPUT] Initializing ReadProvider
[INPUT] Input is Fastq
[INPUT] Estimating parameter from data
[INPUT] Reads found in files: 1
[INPUT] Average read length: 60 (min: 60, max: 62)
[INPUT] Corridor width: 14
[INPUT] Not enough reads to estimate parameter
[INPUT] Sensitivity parameter neither set nor estimated. Falling back to default.
[INPUT] Initializing took 0.004s
[INPUT] Input is Fastq
[MAIN] Core initialization complete
[OPENCL] Available platforms: 1
[OPENCL] AMD Accelerated Parallel Processing
[OPENCL] Selecting OpenCl platform: AMD Accelerated Parallel Processing
[OPENCL] Platform: OpenCL 1.2 AMD-APP (1214.3)
[OPENCL] 1 CPU device found.
[OPENCL] Device 0: AMD Opteron(tm) Processor 6348 (Driver: 1214.3 (sse2,avx,fma4))
[OPENCL] 48 CPU cores available.
[MAIN] Alignments computed: 1
[MAIN] Done (1 reads mapped (100.00%), 0 reads not mapped, 1 lines written)(elapsed: 7.314882s)
systime5.316
time7.44009017944
usrtime2.416
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

/software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/bin-linux/ngm-0.4.11 --output out_ngm_0_4_11.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq --no-progress
memory5586812000
return0
status1
stderr
None
stdout
No protocol specified
[MAIN] NextGenMap 0.4.11
[MAIN] Startup : x64 (build Apr 19 2014 08:01:02)
[MAIN] Starting time: 2018-07-13.18:18:16
[CONFIG] Parameter: --affine 0 --block_multiplier 2 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 4 --dualstrand 1 --fast_pairing 0 --format 1 --gap_extend_penalty 5 --gap_read_penalty 20 --gap_ref_penalty 20 --hard_clip 0 --keep_tags 0 --kmer 13 --kmer_min 0 --kmer_skip 2 --match_bonus 10 --match_bonus_tc 4 --match_bonus_tt 4 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --min_identity 0.650000 --min_insert_size 0 --min_mq 0 --min_residues 0.500000 --min_score 0.000000 --mismatch_penalty 15 --mode 0 --no_progress 1 --no_unal 0 --ocl_threads 1 --output out_ngm_0_4_11.sam --overwrite 1 --pair_score_cutoff 0.900000 --paired 0 --parse_all 1 --pe_delimiter / --qry reads_base.fastq --qry_count -1 --qry_start 0 --ref /project/teaser/genometeaser/references/H_sapiens.fa --ref_mode -1 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --step_count 4 --strata 0 --topn 1
[STATS] Exporting stats at 0x44c22000 (Key 0x7328763d, ID 0x3b8001)
[NGM] Opening for output (SAM): out_ngm_0_4_11.sam
[NGM] NGM Core initialization
[SEQPROV] Init sequence provider.
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/H_sapiens.fa-enc.ngm
[SEQPROV] Reading from disk took 1.21s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/H_sapiens.fa-ht-13-2.ngm
[PREPROCESS] Reading from disk took 3.53s
[INPUT] Initializing ReadProvider
[INPUT] Input is Fastq
[INPUT] Estimating parameter from data
[INPUT] Reads found in files: 1
[INPUT] Average read length: 60 (min: 60, max: 62)
[INPUT] Corridor width: 14
[INPUT] Not enough reads to estimate parameter
[INPUT] Sensitivity parameter neither set nor estimated. Falling back to default.
[INPUT] Initializing took 0.003s
[INPUT] Input is Fastq
[MAIN] Core initialization complete
[OPENCL] Available platforms: 1
[OPENCL] AMD Accelerated Parallel Processing
[OPENCL] Selecting OpenCl platform: AMD Accelerated Parallel Processing
[OPENCL] Platform: OpenCL 1.2 AMD-APP (1214.3)
[OPENCL] 1 CPU device found.
[OPENCL] Device 0: AMD Opteron(tm) Processor 6348 (Driver: 1214.3 (sse2,avx,fma4))
[OPENCL] 48 CPU cores available.
[MAIN] Alignments computed: 1
[MAIN] Done (1 reads mapped (100.00%), 0 reads not mapped, 1 lines written)(elapsed: 7.004920s)
systime5.108
time7.10994911194
usrtime2.236
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

/software/ngm/bin-linux/ngm-0.4.11 --qry2 reads2.fastq --output out_ngm_0_4_11.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --no-progress

command/software/ngm/bin-linux/ngm-0.4.11 --qry2 reads2.fastq --output out_ngm_0_4_11.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --no-progress
memory6657324000
return0
status1
stderr
None
stdout
No protocol specified
[MAIN] NextGenMap 0.4.11
[MAIN] Startup : x64 (build Apr 19 2014 08:01:02)
[MAIN] Starting time: 2018-07-13.18:18:24
[CONFIG] Parameter: --affine 0 --block_multiplier 2 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 4 --dualstrand 1 --fast_pairing 0 --format 1 --gap_extend_penalty 5 --gap_read_penalty 20 --gap_ref_penalty 20 --hard_clip 0 --keep_tags 0 --kmer 13 --kmer_min 0 --kmer_skip 2 --match_bonus 10 --match_bonus_tc 4 --match_bonus_tt 4 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --min_identity 0.650000 --min_insert_size 0 --min_mq 0 --min_residues 0.500000 --min_score 0.000000 --mismatch_penalty 15 --mode 0 --no_progress 1 --no_unal 0 --ocl_threads 1 --output out_ngm_0_4_11.sam --overwrite 1 --pair_score_cutoff 0.900000 --paired 1 --parse_all 1 --pe_delimiter / --qry1 reads1.fastq --qry2 reads2.fastq --qry_count -1 --qry_start 0 --ref /project/teaser/genometeaser/references/H_sapiens.fa --ref_mode -1 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --step_count 4 --strata 0 --topn 1
[STATS] Exporting stats at 0x631ba000 (Key 0x7328763d, ID 0x3b8001)
[NGM] Opening for output (SAM): out_ngm_0_4_11.sam
[NGM] NGM Core initialization
[SEQPROV] Init sequence provider.
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/H_sapiens.fa-enc.ngm
[SEQPROV] Reading from disk took 1.17s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/H_sapiens.fa-ht-13-2.ngm
[PREPROCESS] Reading from disk took 3.55s
[INPUT] Initializing ReadProvider
[INPUT] Input is Fastq
[INPUT] Estimating parameter from data
[INPUT] Reads found in files: 104572
[INPUT] Average read length: 150 (min: 150, max: 152)
[INPUT] Corridor width: 27
[INPUT] Average kmer hits pro read: 38.653854
[INPUT] Max possible kmer hit: 46
[INPUT] Estimated sensitivity: 0.840301
[INPUT] Initializing took 1.679s
[INPUT] Input is Fastq
[INPUT] Input is Fastq
[MAIN] Core initialization complete
[OPENCL] Available platforms: 1
[OPENCL] AMD Accelerated Parallel Processing
[OPENCL] Selecting OpenCl platform: AMD Accelerated Parallel Processing
[OPENCL] Platform: OpenCL 1.2 AMD-APP (1214.3)
[OPENCL] 1 CPU device found.
[OPENCL] Device 0: AMD Opteron(tm) Processor 6348 (Driver: 1214.3 (sse2,avx,fma4))
[OPENCL] 48 CPU cores available.
[MAIN] Valid pairs found: 98.89%
[MAIN] Estimated insert size: 249 bp
[MAIN] Alignments computed: 209027
[MAIN] Done (209004 reads mapped (99.93%), 140 reads not mapped, 209144 lines written)(elapsed: 35.291603s)
systime8.9
time43.0824830532
usrtime100.636
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12