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 Mapped29762594.872%
Wrongly Mapped157825.031%
Not Mapped3060.098%
Total313713100.0%
Read Failure Statistics
Not mapped3060.098%
Missing in mapper output00.0%
Mapped to wrong chromosome117383.742%
Mapped to wrong position40441.289%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment3
Secondary Alignments0
F-Measure0.973700
Precision0.949600
Recall0.999000
Timing
Raw Mapping Time21.479s
Effective Mapping Time19.172s
Effective Init Time2.307s
Effective Time MeasureWall clock
Mapping Time (Wall)21.479s
Mapping Time (CPU)64.046s
Mapping Time (CPU User)60.514s
Mapping Time (CPU System)3.532s
Init Time (Wall)2.307s
Init Time (CPU)2.366s
Init Time (CPU User)1.150s
Init Time (CPU System)1.216s
Additional Information
Mapper Memory Usage7079 MB
Total Test Runtime (Wall)38.094s
Mapper Command Line: 
/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.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/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads_base.fastq --no-progress
memory6006584000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.3

[MAIN] Startup : x64 (build Feb  2 2017 12:01:29)

[MAIN] Starting time: 2017-02-06.14:57:36

[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-0.5.3.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 --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-0.5.3.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-13-2.3.ngm

[PREPROCESS] Reading from disk took 0.87s

[PREPROCESS] Max. k-mer frequency set so 879!

[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: 2.188243s)
systime1.234812
time2.25558114052
usrtime1.151824
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n

/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads_base.fastq --no-progress

command/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads_base.fastq --no-progress
memory6006584000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.3

[MAIN] Startup : x64 (build Feb  2 2017 12:01:29)

[MAIN] Starting time: 2017-02-06.14:57:39

[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-0.5.3.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 --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-0.5.3.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-13-2.3.ngm

[PREPROCESS] Reading from disk took 0.84s

[PREPROCESS] Max. k-mer frequency set so 879!

[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: 2.200185s)
systime1.215815
time2.30718302727
usrtime1.149825
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n

/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads.fastq --no-progress

command/software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads.fastq --no-progress
memory7079184000
return0
status1
stderr

None
stdout

[MAIN] NextGenMap 0.5.3

[MAIN] Startup : x64 (build Feb  2 2017 12:01:29)

[MAIN] Starting time: 2017-02-06.14:57:43

[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-0.5.3.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 --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-0.5.3.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-13-2.3.ngm

[PREPROCESS] Reading from disk took 0.84s

[PREPROCESS] Max. k-mer frequency set so 879!

[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: 313716

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

[INPUT] Corridor width: 20

[INPUT] Average kmer hits pro read: 20.262304

[INPUT] Max possible kmer hit: 29

[INPUT] Estimated sensitivity: 0.698700

[INPUT] Estimating parameter took 1.174s

[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: 313501

[MAIN] Done (313409 reads mapped (99.90%), 307 reads not mapped, 313716 lines written)(elapsed: 20.108500s)
systime3.532462
time21.4788179398
usrtime60.5138
working_directory/project2/NextGenMapTest/Teaser/tests_generated/H2_n