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 Mapped30031595.728%
Wrongly Mapped125183.99%
Not Mapped8830.281%
Total313716100.0%
Read Failure Statistics
Not mapped8830.281%
Missing in mapper output00.0%
Mapped to wrong chromosome87912.802%
Mapped to wrong position37271.188%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.978200
Precision0.960000
Recall0.997100
Timing
Raw Mapping Time110.656s
Effective Mapping Time102.832s
Effective Init Time7.824s
Effective Time MeasureCPU
Mapping Time (Wall)41.080s
Mapping Time (CPU)110.656s
Mapping Time (CPU User)102.024s
Mapping Time (CPU System)8.632s
Init Time (Wall)7.549s
Init Time (CPU)7.824s
Init Time (CPU User)2.220s
Init Time (CPU System)5.604s
Additional Information
Mapper Memory Usage6660 MB
Total Test Runtime (Wall)551.084s
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
memory5586908000
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: 2018-07-13.16:00:26
[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 0x91e02000 (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 133.40s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/H_sapiens.fa-ht-13-2.ngm
[PREPROCESS] Reading from disk took 319.83s
[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: 455.050140s)
systime7.0
time455.16863203
usrtime1.728
working_directory/project/teaser/genometeaser/tests_generated/6996f5893fc23a4f84e9e00364871d38

/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
memory5586744000
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: 2018-07-13.16:08:02
[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 0xc0852000 (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 1.30s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/H_sapiens.fa-ht-13-2.ngm
[PREPROCESS] Reading from disk took 3.86s
[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: 7.422094s)
systime5.604
time7.54914498329
usrtime2.22
working_directory/project/teaser/genometeaser/tests_generated/6996f5893fc23a4f84e9e00364871d38

/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
memory6660688000
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: 2018-07-13.16:08:10
[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 0xdda5a000 (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 1.19s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/H_sapiens.fa-ht-13-2.ngm
[PREPROCESS] Reading from disk took 3.49s
[INPUT] Initializing ReadProvider
[INPUT] Input is Fastq
[INPUT] Estimating parameter from data
[INPUT] Reads found in files: 156858
[INPUT] Average read length: 100 (min: 100, max: 102)
[INPUT] Corridor width: 20
[INPUT] Average kmer hits pro read: 23.239130
[INPUT] Max possible kmer hit: 29
[INPUT] Estimated sensitivity: 0.801349
[INPUT] Initializing took 1.496s
[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: 98.30%
[MAIN] Estimated insert size: 125 bp
[MAIN] Alignments computed: 312942
[MAIN] Done (312833 reads mapped (99.72%), 883 reads not mapped, 313716 lines written)(elapsed: 36.261459s)
systime8.632
time41.0797049999
usrtime102.024
working_directory/project/teaser/genometeaser/tests_generated/6996f5893fc23a4f84e9e00364871d38