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 Mapped29783594.939%
Wrongly Mapped156004.973%
Not Mapped2780.089%
Total313713100.0%
Read Failure Statistics
Not mapped2780.089%
Missing in mapper output00.0%
Mapped to wrong chromosome115543.683%
Mapped to wrong position40461.29%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment3
Secondary Alignments0
F-Measure0.974000
Precision0.950200
Recall0.999100
Timing
Raw Mapping Time20.272s
Effective Mapping Time18.148s
Effective Init Time2.124s
Effective Time MeasureWall clock
Mapping Time (Wall)20.272s
Mapping Time (CPU)61.385s
Mapping Time (CPU User)57.932s
Mapping Time (CPU System)3.452s
Init Time (Wall)2.124s
Init Time (CPU)2.150s
Init Time (CPU User)1.001s
Init Time (CPU System)1.149s
Additional Information
Mapper Memory Usage6648 MB
Total Test Runtime (Wall)36.887s
Mapper Command Line: 
/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads.fastq --no-progress
Errors and Warnings
No problems were encountered.
Subprocess Log

/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads_base.fastq --no-progress
memory5575856000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

[MAIN] Startup : x64 (build Jun 26 2015 16:16:32)

[MAIN] Starting time: 2017-01-21.04:30:49

[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_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 4 --match_bonus_tt 4 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --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-0.4.13.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 /project2/NextGenMapTest/Teaser/references/GRCh37.fa --ref_mode -1 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --step_count 4 --strata 0 --topn 1 --update_check 0

[NGM] Opening for output (SAM): out_ngm-0.4.13.sam

[SEQPROV] Reading encoded reference from /project2/NextGenMapTest/Teaser/references/GRCh37.fa-enc.2.ngm

[SEQPROV] Reading 3137 Mbp from disk took 0.27s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/GRCh37.fa-ht-13-2.2.ngm

[PREPROCESS] Reading from disk took 0.77s

[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 0.002s

[INPUT] Input is Fastq

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

[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: Intel(R) Core(TM) i5-2500K CPU @ 3.30GHz (Driver: 1214.3 (sse2,avx))

[OPENCL] 4 CPU cores available.

[MAIN] Alignments computed: 1

[MAIN] Done (1 reads mapped (100.00%), 0 reads not mapped, 1 lines written)(elapsed: 2.044041s)

[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)
systime1.17782
time2.24884295464
usrtime0.978851
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n

/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads_base.fastq --no-progress
memory5575784000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

[MAIN] Startup : x64 (build Jun 26 2015 16:16:32)

[MAIN] Starting time: 2017-01-21.04:30:52

[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_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 4 --match_bonus_tt 4 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --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-0.4.13.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 /project2/NextGenMapTest/Teaser/references/GRCh37.fa --ref_mode -1 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --step_count 4 --strata 0 --topn 1 --update_check 0

[NGM] Opening for output (SAM): out_ngm-0.4.13.sam

[SEQPROV] Reading encoded reference from /project2/NextGenMapTest/Teaser/references/GRCh37.fa-enc.2.ngm

[SEQPROV] Reading 3137 Mbp from disk took 0.26s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/GRCh37.fa-ht-13-2.2.ngm

[PREPROCESS] Reading from disk took 0.76s

[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

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

[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: Intel(R) Core(TM) i5-2500K CPU @ 3.30GHz (Driver: 1214.3 (sse2,avx))

[OPENCL] 4 CPU cores available.

[MAIN] Alignments computed: 1

[MAIN] Done (1 reads mapped (100.00%), 0 reads not mapped, 1 lines written)(elapsed: 2.086866s)

[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)
systime1.148825
time2.12410998344
usrtime1.000847
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n

/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads.fastq --no-progress

command/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads.fastq --no-progress
memory6648848000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

[MAIN] Startup : x64 (build Jun 26 2015 16:16:32)

[MAIN] Starting time: 2017-01-21.04:30:55

[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_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 4 --match_bonus_tt 4 --max_cmrs 2147483647 --max_equal 1 --max_insert_size 1000 --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-0.4.13.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 /project2/NextGenMapTest/Teaser/references/GRCh37.fa --ref_mode -1 --silent_clip 0 --skip_mate_check 0 --skip_save 0 --step_count 4 --strata 0 --topn 1 --update_check 0

[NGM] Opening for output (SAM): out_ngm-0.4.13.sam

[SEQPROV] Reading encoded reference from /project2/NextGenMapTest/Teaser/references/GRCh37.fa-enc.2.ngm

[SEQPROV] Reading 3137 Mbp from disk took 0.26s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/GRCh37.fa-ht-13-2.2.ngm

[PREPROCESS] Reading from disk took 0.76s

[INPUT] Input is Fastq

[INPUT] Estimating parameter from data

[INPUT] Reads found in files: 313716

[INPUT] Average read length: 100 (min: 100, max: 102)

[INPUT] Corridor width: 20

[INPUT] Average kmer hits pro read: 20.357388

[INPUT] Max possible kmer hit: 29

[INPUT] Estimated sensitivity: 0.701979

[INPUT] Estimating parameter took 1.155s

[INPUT] Input is Fastq

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

Setting of real/effective user Id to 0/0 failed

FATAL: Module fglrx not found.

Error! Fail to load fglrx kernel module! Maybe you can switch to root user to load kernel module directly

[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: Intel(R) Core(TM) i5-2500K CPU @ 3.30GHz (Driver: 1214.3 (sse2,avx))

[OPENCL] 4 CPU cores available.

[MAIN] Alignments computed: 313524

[MAIN] Done (313437 reads mapped (99.91%), 279 reads not mapped, 313716 lines written)(elapsed: 18.868048s)

[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)
systime3.452475
time20.2716720104
usrtime57.932192
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n