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 Mapped22008391.877%
Wrongly Mapped194368.114%
Not Mapped230.01%
Total239542100.0%
Read Failure Statistics
Not mapped230.01%
Missing in mapper output00.0%
Mapped to wrong chromosome102914.296%
Mapped to wrong position91453.818%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.957700
Precision0.918900
Recall0.999900
Timing
Raw Mapping Time40.336s
Effective Mapping Time37.500s
Effective Init Time2.836s
Effective Time MeasureCPU
Mapping Time (Wall)15.373s
Mapping Time (CPU)40.336s
Mapping Time (CPU User)38.533s
Mapping Time (CPU System)1.803s
Init Time (Wall)2.766s
Init Time (CPU)2.836s
Init Time (CPU User)1.845s
Init Time (CPU System)0.991s
Additional Information
Mapper Memory Usage2048 MB
Total Test Runtime (Wall)35.126s
Mapper Command Line: 
/project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -t 4 --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: 2017-05-17.23:41:53
[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 0.04s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/D_melanogaster.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.34s
[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.
systime0
time0.624102830887
usrtime0
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae

/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
memory946568000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-17.23:41:55
[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 0.03s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/D_melanogaster.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.33s
[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 0.004s
[INPUT] Input is Fastq
[OPENCL] Available platforms: 2
[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: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz (Driver: 1214.3 (sse2))
[OPENCL] 24 CPU cores available.
[MAIN] Alignments computed: 1
[MAIN] Done (0 reads mapped (0.00%), 1 reads not mapped, 1 lines written)(elapsed: 1.899691s)
systime0.893864
time1.98434996605
usrtime1.401786
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae

/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
memory950112000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-17.23:41:57
[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 0.03s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/D_melanogaster.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.38s
[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 0.000s
[INPUT] Input is Fastq
[OPENCL] Available platforms: 2
[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: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz (Driver: 1214.3 (sse2))
[OPENCL] 24 CPU cores available.
[MAIN] Alignments computed: 1
[MAIN] Done (0 reads mapped (0.00%), 1 reads not mapped, 1 lines written)(elapsed: 2.644100s)
systime0.990849
time2.76551198959
usrtime1.844719
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae

/project/teaser/genometeaser/software/ngm/ngm --qry2 reads2.fastq --output out_ngm.sam --qry1 reads1.fastq --ref /project/teaser/genometeaser/references/D_melanogaster.fasta -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/D_melanogaster.fasta -t 4 --no-progress
memory2048672000
return0
status1
stderr
None
stdout
[MAIN] NextGenMap 0.5.3
[MAIN] Startup : x64 (build Jan 31 2017 16:20:45)
[MAIN] Starting time: 2017-05-17.23:42:00
[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 1 --parse_all 1 --pe_delimiter / --qry1 reads1.fastq --qry2 reads2.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 0.04s
[PREPROCESS] Reading RefTable from /project/teaser/genometeaser/references/D_melanogaster.fasta-ht-13-2.3.ngm
[PREPROCESS] Reading from disk took 0.43s
[PREPROCESS] Max. k-mer frequency set so 100!
[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: 119771
[INPUT] Average read length: 150 (min: 150, max: 152)
[INPUT] Corridor width: 27
[INPUT] Average kmer hits pro read: 35.252094
[INPUT] Max possible kmer hit: 46
[INPUT] Estimated sensitivity: 0.766350
[INPUT] Estimating parameter took 0.514s
[INPUT] Input is Fastq
[INPUT] Input is Fastq
[OPENCL] Available platforms: 2
[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: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz (Driver: 1214.3 (sse2))
[OPENCL] 24 CPU cores available.
[MAIN] Valid pairs found: 99.67%
[MAIN] Estimated insert size: 200 bp
[MAIN] Alignments computed: 239532
[MAIN] Done (239519 reads mapped (99.99%), 23 reads not mapped, 239542 lines written)(elapsed: 13.498312s)
systime1.802725
time15.3732199669
usrtime38.533142
working_directory/project/teaser/genometeaser/tests_generated/75a17aa3ae45687f5c9f13afd04e2aae