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 Mapped29629291.856%
Wrongly Mapped262358.133%
Not Mapped340.011%
Total322561100.0%
Read Failure Statistics
Not mapped340.011%
Missing in mapper output00.0%
Mapped to wrong chromosome147174.563%
Mapped to wrong position115183.571%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.957600
Precision0.918700
Recall0.999900
Timing
Raw Mapping Time60.052s
Effective Mapping Time57.485s
Effective Init Time2.568s
Effective Time MeasureWall clock
Mapping Time (Wall)60.052s
Mapping Time (CPU)208.095s
Mapping Time (CPU User)196.722s
Mapping Time (CPU System)11.373s
Init Time (Wall)2.568s
Init Time (CPU)2.706s
Init Time (CPU User)1.260s
Init Time (CPU System)1.446s
Additional Information
Mapper Memory Usage7928 MB
Total Test Runtime (Wall)101.214s
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
memory6921004000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.2

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

[MAIN] Starting time: 2017-01-21.04:53:17

[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 7.07s

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

[PREPROCESS] Reading from disk took 6.42s

[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: 15.520033s)
systime3.010542
time15.7481319904
usrtime1.365792
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_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
memory6852452000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.2

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

[MAIN] Starting time: 2017-01-21.04:53:33

[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 0.43s

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

[PREPROCESS] Reading from disk took 0.94s

[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 0.000s

[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: 2.537727s)
systime1.44578
time2.56760692596
usrtime1.259808
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_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
memory7928628000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.2

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

[MAIN] Starting time: 2017-01-21.04:53:36

[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 0.41s

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

[PREPROCESS] Reading from disk took 0.92s

[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: 19.484470

[INPUT] Max possible kmer hit: 46

[INPUT] Estimated sensitivity: 0.423575

[INPUT] Estimating parameter took 1.507s

[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: 58.311310s)
systime11.373271
time60.0524199009
usrtime196.722093
working_directory/project2/NextGenMapTest/Teaser/tests_generated/M2_n