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 Mapped30076293.242%
Wrongly Mapped206516.402%
Not Mapped11480.356%
Total322561100.0%
Read Failure Statistics
Not mapped11480.356%
Missing in mapper output00.0%
Mapped to wrong chromosome99493.084%
Mapped to wrong position107023.318%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.965000
Precision0.935700
Recall0.996200
Timing
Raw Mapping Time53.566s
Effective Mapping Time6.619s
Effective Init Time46.947s
Effective Time MeasureWall clock
Mapping Time (Wall)53.566s
Mapping Time (CPU)131.062s
Mapping Time (CPU User)122.392s
Mapping Time (CPU System)8.670s
Init Time (Wall)46.947s
Init Time (CPU)7.649s
Init Time (CPU User)1.122s
Init Time (CPU System)6.527s
Additional Information
Mapper Memory Usage7540 MB
Total Test Runtime (Wall)184.465s
Mapper Command Line: 
/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -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/m_musculus.fasta -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/m_musculus.fasta -t 4 --qry reads_base.fastq --no-progress
memory6528304000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

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

[MAIN] Starting time: 2017-01-21.04:31:26

[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/m_musculus.fasta --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/m_musculus.fasta-enc.2.ngm

[SEQPROV] Reading 4838 Mbp from disk took 26.54s

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

[PREPROCESS] Reading from disk took 41.20s

[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: 69.303215s)

[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)
systime9.778513
time69.3919849396
usrtime1.132827
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_n

/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -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/m_musculus.fasta -t 4 --qry reads_base.fastq --no-progress
memory6505700000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

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

[MAIN] Starting time: 2017-01-21.04:32:37

[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/m_musculus.fasta --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/m_musculus.fasta-enc.2.ngm

[SEQPROV] Reading 4838 Mbp from disk took 16.63s

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

[PREPROCESS] Reading from disk took 28.75s

[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 0.001s

[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: 46.687824s)

[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)
systime6.527007
time46.9467279911
usrtime1.121829
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_n

/software/ngm/bin-linux/ngm-0.4.13 --output out_ngm-0.4.13.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -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/m_musculus.fasta -t 4 --qry reads.fastq --no-progress
memory7540972000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

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

[MAIN] Starting time: 2017-01-21.04:33:24

[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/m_musculus.fasta --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/m_musculus.fasta-enc.2.ngm

[SEQPROV] Reading 4838 Mbp from disk took 8.80s

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

[PREPROCESS] Reading from disk took 6.17s

[INPUT] Input is Fastq

[INPUT] Estimating parameter from data

[INPUT] Reads found in files: 322561

[INPUT] Average read length: 150 (min: 150, max: 152)

[INPUT] Corridor width: 27

[INPUT] Average kmer hits pro read: 35.776379

[INPUT] Max possible kmer hit: 46

[INPUT] Estimated sensitivity: 0.777747

[INPUT] Estimating parameter took 2.105s

[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: 321575

[MAIN] Done (321413 reads mapped (99.64%), 1148 reads not mapped, 322561 lines written)(elapsed: 51.770123s)

[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)
systime8.669682
time53.5657689571
usrtime122.392393
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_n