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 Mapped52970788.453%
Wrongly Mapped6850511.439%
Not Mapped6460.108%
Total598858100.0%
Read Failure Statistics
Not mapped6460.108%
Missing in mapper output00.0%
Mapped to wrong chromosome406296.784%
Mapped to wrong position278764.655%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.938700
Precision0.885500
Recall0.998800
Timing
Raw Mapping Time111.548s
Effective Mapping Time87.016s
Effective Init Time24.532s
Effective Time MeasureCPU
Mapping Time (Wall)66.673s
Mapping Time (CPU)111.548s
Mapping Time (CPU User)81.916s
Mapping Time (CPU System)29.632s
Init Time (Wall)16.842s
Init Time (CPU)24.532s
Init Time (CPU User)3.552s
Init Time (CPU System)20.980s
Additional Information
Mapper Memory Usage2049 MB
Total Test Runtime (Wall)256.667s
Mapper Command Line: 
/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads.fastq --no-progress
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/D_melanogaster.fasta

command/project/teaser/genometeaser/software/ngm/ngm --ref /project/teaser/genometeaser/references/D_melanogaster.fasta
return1
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-08-19.01:04:44
[CONFIG] Parameter: --affine 0 --argos_min_score 0 --bin_size 2 --block_multiplier 2 --bs_cutoff 6 --bs_mapping 0 --cpu_threads 1 --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 0 --no_unal 0 --ocl_threads 1 --overwrite 1 --pair_score_cutoff 0.900000 --paired 0 --parse_all 1 --pe_delimiter / --qry_count -1 --qry_start 0 --ref /project/teaser/genometeaser/references/D_melanogaster.fasta --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] Wrinting output (SAM) to stdout
[SEQPROV] Reading encoded reference from /project/teaser/genometeaser/references/D_melanogaster.fasta-enc.2.ngm
[SEQPROV] Reading 145 Mbp from disk took 6.24s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/D_melanogaster.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 49.84s
[PREPROCESS] Max. k-mer frequency set so 100!
[MAIN] Finished building hash table.
[MAIN] No qry file specified. If you want to map single-end data use -q/--qry. If you want to map paired-end data, either use -q/--qry and -p or --qry1 and --qry2.
[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)
systime0
time56.9885869026
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3

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

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress
memory1477604000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-08-19.01:05:41
[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/D_melanogaster.fasta --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/D_melanogaster.fasta-enc.2.ngm
[SEQPROV] Reading 145 Mbp from disk took 0.58s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/D_melanogaster.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 6.03s
[PREPROCESS] Max. k-mer frequency set so 100!
[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 0.008s
[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 (0 reads mapped (0.00%), 1 reads not mapped, 1 lines written)(elapsed: 19.152079s)
[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)
systime19.752
time19.4022610188
usrtime3.312
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3

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

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress
memory1370504000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-08-19.01:06:01
[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/D_melanogaster.fasta --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/D_melanogaster.fasta-enc.2.ngm
[SEQPROV] Reading 145 Mbp from disk took 0.74s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/D_melanogaster.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 6.28s
[PREPROCESS] Max. k-mer frequency set so 100!
[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 0.006s
[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 (0 reads mapped (0.00%), 1 reads not mapped, 1 lines written)(elapsed: 16.554470s)
[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)
systime20.98
time16.8423361778
usrtime3.552
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3

/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads.fastq --no-progress

command/project/teaser/genometeaser/software/ngm/ngm --output out_ngm.sam --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --qry reads.fastq --no-progress
memory2049456000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-08-19.01:06:18
[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.fastq --qry_count -1 --qry_start 0 --ref /project/teaser/genometeaser/references/D_melanogaster.fasta --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/D_melanogaster.fasta-enc.2.ngm
[SEQPROV] Reading 145 Mbp from disk took 0.70s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/D_melanogaster.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 6.35s
[PREPROCESS] Max. k-mer frequency set so 100!
[INPUT] Input is single end data.
[INPUT] Opening file reads.fastq for reading
[INPUT] Input is Fastq
[INPUT] Estimating parameter from data
[INPUT] Reads found in files: 598858
[INPUT] Average read length: 60 (min: 60, max: 62)
[INPUT] Corridor width: 14
[INPUT] Average kmer hits pro read: 14.451505
[INPUT] Max possible kmer hit: 16
[INPUT] Estimated sensitivity: 0.900000
[INPUT] Estimating parameter took 3.250s
[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: 598270
[MAIN] Done (598212 reads mapped (99.89%), 646 reads not mapped, 598858 lines written)(elapsed: 54.664604s)
[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)
systime29.632
time66.6733429432
usrtime81.916
working_directory/project/teaser/genometeaser/tests_generated/0bc744fc434e081e5d0279784d2334f3