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 Mapped30074393.236%
Wrongly Mapped206946.416%
Not Mapped11240.348%
Total322561100.0%
Read Failure Statistics
Not mapped11240.348%
Missing in mapper output00.0%
Mapped to wrong chromosome99913.097%
Mapped to wrong position107033.318%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.965000
Precision0.935600
Recall0.996300
Timing
Raw Mapping Time72.372s
Effective Mapping Time11.365s
Effective Init Time61.006s
Effective Time MeasureWall clock
Mapping Time (Wall)72.372s
Mapping Time (CPU)138.142s
Mapping Time (CPU User)128.887s
Mapping Time (CPU System)9.255s
Init Time (Wall)61.006s
Init Time (CPU)11.479s
Init Time (CPU User)1.353s
Init Time (CPU System)10.126s
Additional Information
Mapper Memory Usage7927 MB
Total Test Runtime (Wall)218.823s
Mapper Command Line: 
/software/ngm/dev/ngm-0.5.2/ngm --output out_ngm-0.5.2.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/dev/ngm-0.5.2/ngm --output out_ngm-0.5.2.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/dev/ngm-0.5.2/ngm --output out_ngm-0.5.2.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads_base.fastq --no-progress
memory6900436000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.2

[MAIN] Startup : x64 (build Nov 24 2016 17:40:01)

[MAIN] Starting time: 2017-01-21.04:49:38

[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-0.5.2.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 --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-0.5.2.sam

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

[SEQPROV] Reading 4838 Mbp from disk took 23.18s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/m_musculus.fasta-ht-13-2.3.ngm

[PREPROCESS] Reading from disk took 45.23s

[PREPROCESS] Max. k-mer frequency set so 1007!

[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

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: 70.413681s)
systime8.778665
time70.6769990921
usrtime1.399787
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_n

/software/ngm/dev/ngm-0.5.2/ngm --output out_ngm-0.5.2.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/dev/ngm-0.5.2/ngm --output out_ngm-0.5.2.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads_base.fastq --no-progress
memory6951176000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.2

[MAIN] Startup : x64 (build Nov 24 2016 17:40:01)

[MAIN] Starting time: 2017-01-21.04:50:49

[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 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-0.5.2.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 --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-0.5.2.sam

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

[SEQPROV] Reading 4838 Mbp from disk took 18.93s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/m_musculus.fasta-ht-13-2.3.ngm

[PREPROCESS] Reading from disk took 39.87s

[PREPROCESS] Max. k-mer frequency set so 1007!

[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 0.002s

[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: 60.778400s)
systime10.12646
time61.0061929226
usrtime1.352794
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_n

/software/ngm/dev/ngm-0.5.2/ngm --output out_ngm-0.5.2.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads.fastq --no-progress

command/software/ngm/dev/ngm-0.5.2/ngm --output out_ngm-0.5.2.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads.fastq --no-progress
memory7927648000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.2

[MAIN] Startup : x64 (build Nov 24 2016 17:40:01)

[MAIN] Starting time: 2017-01-21.04:51:50

[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-0.5.2.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 --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-0.5.2.sam

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

[SEQPROV] Reading 4838 Mbp from disk took 10.20s

[PREPROCESS] Reading RefTable from /project2/NextGenMapTest/Teaser/references/m_musculus.fasta-ht-13-2.3.ngm

[PREPROCESS] Reading from disk took 23.10s

[PREPROCESS] Max. k-mer frequency set so 1007!

[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: 322561

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

[INPUT] Corridor width: 27

[INPUT] Average kmer hits pro read: 35.807438

[INPUT] Max possible kmer hit: 46

[INPUT] Estimated sensitivity: 0.778423

[INPUT] Estimating parameter took 1.834s

[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: 321595

[MAIN] Done (321437 reads mapped (99.65%), 1124 reads not mapped, 322561 lines written)(elapsed: 70.577148s)
systime9.254593
time72.3715648651
usrtime128.887406
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M1_n