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 Mapped39686494.878%
Wrongly Mapped187574.484%
Not Mapped26670.638%
Total418288100.0%
Read Failure Statistics
Not mapped26670.638%
Missing in mapper output00.0%
Mapped to wrong chromosome136693.268%
Mapped to wrong position50881.216%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.973700
Precision0.954900
Recall0.993300
Timing
Raw Mapping Time290.956s
Effective Mapping Time163.564s
Effective Init Time127.392s
Effective Time MeasureCPU
Mapping Time (Wall)167.560s
Mapping Time (CPU)290.956s
Mapping Time (CPU User)127.900s
Mapping Time (CPU System)163.056s
Init Time (Wall)117.920s
Init Time (CPU)127.392s
Init Time (CPU User)2.256s
Init Time (CPU System)125.136s
Additional Information
Mapper Memory Usage7090 MB
Total Test Runtime (Wall)858.281s
Mapper Command Line: 
/project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.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

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

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq --no-progress
memory6626656000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-09-09.17:43:25
[CONFIG] Parameter: --affine 0 --argos_min_score 0 --bin_size 2 --block_multiplier 2 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 4 --dualstrand 1 --fast 0 --fast_pairing 0 --force_rlength_check 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 2 --match_bonus_tt 10 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --max_polya -1 --max_read_length 0 --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.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 --sensitive 0 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --slam_seq 0 --step_count 4 --strata 0 --topn 1 --trim5 0 --update_check 0 --very_fast 0 --very_sensitive 0
[NGM] Opening for output (SAM): out_ngm.sam
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/H_sapiens.fa-enc.2.ngm
[SEQPROV] Reading 3137 Mbp from disk took 133.37s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/H_sapiens.fa-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 362.86s
[PREPROCESS] Max. k-mer frequency set so 879!
[INPUT] Input is single end data.
[INPUT] Opening file reads_base.fastq for reading
[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] Estimating parameter took 0.005s
[INPUT] Input is Fastq
No protocol specified
[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: 513.920471s)
[UPDATE_CHECK] Your version of NGM is more than 6 months old - a newer version may be available. (For performing an automatic check use --update-check)
systime123.4
time515.349156141
usrtime2.596
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1

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

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --qry reads_base.fastq --no-progress
memory6374620000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-09-09.17:52:00
[CONFIG] Parameter: --affine 0 --argos_min_score 0 --bin_size 2 --block_multiplier 2 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 4 --dualstrand 1 --fast 0 --fast_pairing 0 --force_rlength_check 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 2 --match_bonus_tt 10 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --max_polya -1 --max_read_length 0 --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.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 --sensitive 0 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --slam_seq 0 --step_count 4 --strata 0 --topn 1 --trim5 0 --update_check 0 --very_fast 0 --very_sensitive 0
[NGM] Opening for output (SAM): out_ngm.sam
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/H_sapiens.fa-enc.2.ngm
[SEQPROV] Reading 3137 Mbp from disk took 27.58s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/H_sapiens.fa-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 73.22s
[PREPROCESS] Max. k-mer frequency set so 879!
[INPUT] Input is single end data.
[INPUT] Opening file reads_base.fastq for reading
[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] Estimating parameter took 0.005s
[INPUT] Input is Fastq
No protocol specified
[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: 116.533478s)
[UPDATE_CHECK] Your version of NGM is more than 6 months old - a newer version may be available. (For performing an automatic check use --update-check)
systime125.136
time117.919987917
usrtime2.256
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1

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

command/project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/H_sapiens.fa -t 4 --no-progress
memory7090612000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-09-09.17:53:59
[CONFIG] Parameter: --affine 0 --argos_min_score 0 --bin_size 2 --block_multiplier 2 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 4 --dualstrand 1 --fast 0 --fast_pairing 0 --force_rlength_check 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 2 --match_bonus_tt 10 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --max_polya -1 --max_read_length 0 --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.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 --sensitive 0 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --slam_seq 0 --step_count 4 --strata 0 --topn 1 --trim5 0 --update_check 0 --very_fast 0 --very_sensitive 0
[NGM] Opening for output (SAM): out_ngm.sam
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/H_sapiens.fa-enc.2.ngm
[SEQPROV] Reading 3137 Mbp from disk took 26.97s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/H_sapiens.fa-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 72.58s
[PREPROCESS] Max. k-mer frequency set so 879!
[INPUT] Input is paired end data.
[INPUT] Opening file reads1.fastq for reading
[INPUT] Opening file reads2.fastq for reading
[INPUT] Input is Fastq
[INPUT] Estimating parameter from data
[INPUT] Reads found in files: 209144
[INPUT] Average read length: 75 (min: 75, max: 76)
[INPUT] Corridor width: 16
[INPUT] Average kmer hits pro read: 16.894735
[INPUT] Max possible kmer hit: 21
[INPUT] Estimated sensitivity: 0.804511
[INPUT] Estimating parameter took 1.847s
[INPUT] Input is Fastq
[INPUT] Input is Fastq
No protocol specified
[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: 95.98%
[MAIN] Estimated insert size: 448 bp
[MAIN] Alignments computed: 415868
[MAIN] Done (415621 reads mapped (99.36%), 2667 reads not mapped, 418288 lines written)(elapsed: 159.636169s)
[UPDATE_CHECK] Your version of NGM is more than 6 months old - a newer version may be available. (For performing an automatic check use --update-check)
systime163.056
time167.559551954
usrtime127.9
working_directory/project/teaser/genometeaser/tests_generated/a5e600139d12b867a2e96eee861838f1