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 Mapped29627391.85%
Wrongly Mapped262548.139%
Not Mapped340.011%
Total322561100.0%
Read Failure Statistics
Not mapped340.011%
Missing in mapper output00.0%
Mapped to wrong chromosome147404.57%
Mapped to wrong position115143.57%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.957500
Precision0.918600
Recall0.999900
Timing
Raw Mapping Time56.284s
Effective Mapping Time54.090s
Effective Init Time2.194s
Effective Time MeasureWall clock
Mapping Time (Wall)56.284s
Mapping Time (CPU)198.828s
Mapping Time (CPU User)187.642s
Mapping Time (CPU System)11.185s
Init Time (Wall)2.194s
Init Time (CPU)2.375s
Init Time (CPU User)1.042s
Init Time (CPU System)1.333s
Additional Information
Mapper Memory Usage7548 MB
Total Test Runtime (Wall)88.162s
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
memory6468960000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

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

[MAIN] Starting time: 2017-01-21.04:34:31

[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 3.98s

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

[PREPROCESS] Reading from disk took 1.32s

[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: 6.308445s)

[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)
systime1.44278
time6.52404212952
usrtime1.042841
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_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
memory6468960000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

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

[MAIN] Starting time: 2017-01-21.04:34:38

[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_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 0.41s

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

[PREPROCESS] Reading from disk took 0.84s

[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: 2.159511s)

[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)
systime1.332797
time2.1940870285
usrtime1.041841
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_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
memory7548652000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.4.13

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

[MAIN] Starting time: 2017-01-21.04:34:41

[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_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 0.40s

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

[PREPROCESS] Reading from disk took 0.84s

[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: 19.475155

[INPUT] Max possible kmer hit: 46

[INPUT] Estimated sensitivity: 0.423373

[INPUT] Estimating parameter took 1.653s

[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: 322560

[MAIN] Done (322527 reads mapped (99.99%), 34 reads not mapped, 322561 lines written)(elapsed: 54.594990s)

[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)
systime11.185299
time56.2838001251
usrtime187.642474
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_n