Tests Overview
This benchmark contains multiple data sets. Use the links in the list below to view results for an individual data set, or navigate this page to compare mapper performance across all data sets.
70 tests executed, 1 fail, 0 aborted, 0 errors total.Errors and Warnings
No problems were encountered.
Results: Correctly Mapped Reads
Results: Correct/s
Results: Precision
Results: Recall
Results: F-Measure
Raw Results
Setup
This section contains information about the benchmarking process itself and can be shared in order to reproduce results and diagnose problems.
| Teaser Accession | teaser_paper |
|---|---|
| Report timestamp | Mon Feb 6 15:11:49 2017 |
| Framework Version | 1.2-public-vevev | Framework Working Directory | /project2/NextGenMapTest/Teaser |
| Framework Command Line | ./teaser.py -tc 4 setups/teaser-paper.yaml |
| Benchmark Configuration | |
description: Examples showcasing mapper differences across datasets
include: [base.yaml, base_mappers.yaml, base_ngm.yaml, base_teaser.yaml]
report: {directory: /home/CIBIV/philipp_/public_html/teaser/report, name: teaser_paper}
sub_max_memory: 17000
teaser:
dwgsim_path: software/dwgsim
mason_path: software/mason
reference_directory: references
test_directory: tests_generated
tests:
D1_n: {order: 3, paired: false, platform: illumina, read_length: 150, reference: d_melanogaster.fasta,
simulator: mason, title: D1}
D2_n: {mutation_rate: 0.05, order: 5, paired: false, platform: illumina, read_length: 150,
reference: d_melanogaster.fasta, simulator: mason, title: D2}
D3_n: {error_rate_mult: 2, order: 7, paired: false, platform: ion_torrent, read_length: 200,
reference: d_melanogaster.fasta, simulator: dwgsim, title: D3}
D4_n: {order: 9, paired: false, platform: illumina, read_length: 22, reference: d_melanogaster.fasta,
simulator: mason, title: D4}
H1_n: {mutation_indel_frac: 0.3, mutation_rate: 0.001, order: 1, paired: true,
platform: illumina, read_length: 100, reference: GRCh37.fa, simulator: dwgsim,
title: H1}
H2_n: {mutation_indel_frac: 0.7, mutation_rate: 0.001, order: 2, paired: false,
platform: illumina, read_length: 100, reference: GRCh37.fa, simulator: dwgsim,
title: H2}
M1_n: {order: 4, paired: false, platform: illumina, read_length: 150, reference: m_musculus.fasta,
simulator: mason, title: M1}
M2_n: {mutation_rate: 0.05, order: 6, paired: false, platform: illumina, read_length: 150,
reference: m_musculus.fasta, simulator: mason, title: M2}
M3_n: {error_rate_mult: 2, order: 8, paired: false, platform: ion_torrent, read_length: 200,
reference: m_musculus.fasta, simulator: dwgsim, title: M3}
M4_n: {order: 10, paired: false, platform: illumina, read_length: 22, reference: m_musculus.fasta,
simulator: mason, title: M4}
test_directories: [tests_base, tests_generated]
test_mappers: [bowtie2, bwamem, bwa, bwasw, ngm-0.4.13, ngm-0.5.2, ngm-0.5.3]
threads: 4
title: Teaser Example Dataset Evaluation
| |
Log
[14:44:44] [Main ] framework cmd: ./teaser.py -tc 4 setups/teaser-paper.yaml [14:44:44] [Main ] framework hash: vevev [14:44:44] [Main ] deployment mode: production (False) [14:44:44] [Main ] Teaser Example Dataset Evaluation - "Examples showcasing mapper differences across datasets" [14:44:44] [Main ] Using Teaser for data set creation [14:44:45] [Teaser ] Init. Creating 10 test datasets. [14:44:45] [Teaser ] Data set H1_n already exists, not creating. [14:44:45] [Teaser ] Data set H2_n already exists, not creating. [14:44:45] [Teaser ] Data set D1_n already exists, not creating. [14:44:45] [Teaser ] Data set M1_n already exists, not creating. [14:44:45] [Teaser ] Data set D2_n already exists, not creating. [14:44:45] [Teaser ] Data set M2_n already exists, not creating. [14:44:45] [Teaser ] Data set D3_n already exists, not creating. [14:44:45] [Teaser ] Data set M3_n already exists, not creating. [14:44:45] [Teaser ] Data set D4_n already exists, not creating. [14:44:45] [Teaser ] Data set M4_n already exists, not creating. [14:44:45] [Main ] Data set creation completed [14:44:45] [Main ] [14:44:45] [Load H1_n] Loading cached version of H1_n/project2/NextGenMapTest/Teaser/cache/dev_7a43bbae2bfb496b3a49f8ce837cba52.test [14:44:45] [Load H2_n] Loading cached version of H2_n /project2/NextGenMapTest/Teaser/cache/dev_e9c9098d6520a6c716d7251658fd0161.test [14:44:45] [Load D1_n] Loading cached version of D1_n /project2/NextGenMapTest/Teaser/cache/dev_12e63ecb31003284b06189460a37467d.test [14:44:45] [Load M1_n] Loading cached version of M1_n /project2/NextGenMapTest/Teaser/cache/dev_a3d77a467bcebbc0c775de7e16d3960d.test [14:44:45] [Load D2_n] Loading cached version of D2_n /project2/NextGenMapTest/Teaser/cache/dev_87b86c3e9430026218ca832b37d0d1fd.test [14:44:45] [Load M2_n] Loading cached version of M2_n /project2/NextGenMapTest/Teaser/cache/dev_2124a8d94b213493303518a19cacaf04.test [14:44:46] [Load D3_n] Loading cached version of D3_n /project2/NextGenMapTest/Teaser/cache/dev_28ae23b7277e6e48ac855033894441c2.test [14:44:46] [Load M3_n] Loading cached version of M3_n /project2/NextGenMapTest/Teaser/cache/dev_375053ad3998b2c6eefa7660f6abfb99.test [14:44:46] [Load D4_n] Loading cached version of D4_n /project2/NextGenMapTest/Teaser/cache/dev_f1e0e35b56faa85742356b08f161a9ab.test [14:44:46] [Load M4_n] Loading cached version of M4_n /project2/NextGenMapTest/Teaser/cache/dev_deb33f4b50daf7d7315ec83bc0168a99.test [14:44:46] [Load H1_n] Loading cached version of H1_n /project2/NextGenMapTest/Teaser/cache/dev_80165fb83754985847fb16c2a8b3b929.test [14:44:46] [Load H2_n] Loading cached version of H2_n /project2/NextGenMapTest/Teaser/cache/dev_842b40c86626429e2b16c719383d792a.test [14:44:47] [Load D1_n] Loading cached version of D1_n /project2/NextGenMapTest/Teaser/cache/dev_061a79a9deed434860b49da85a112c71.test [14:44:47] [Load M1_n] Loading cached version of M1_n /project2/NextGenMapTest/Teaser/cache/dev_8705e8d3f929d74c4ff322d938fa1dde.test [14:44:47] [Load D2_n] Loading cached version of D2_n /project2/NextGenMapTest/Teaser/cache/dev_d03be6eefbe9557f4721e31b3e9d9ca7.test [14:44:47] [Load M2_n] Loading cached version of M2_n /project2/NextGenMapTest/Teaser/cache/dev_ca540cd6f24c7ee9b5e887c509ca1b5f.test [14:44:47] [Load D3_n] Loading cached version of D3_n /project2/NextGenMapTest/Teaser/cache/dev_9998123d129bc489ac2c50ccec8e9c83.test [14:44:47] [Load M3_n] Loading cached version of M3_n /project2/NextGenMapTest/Teaser/cache/dev_261e90bb19c56e32d19e650e3314d4a0.test [14:44:47] [Load D4_n] Loading cached version of D4_n /project2/NextGenMapTest/Teaser/cache/dev_546eee5450a2700efdbec16bb1592e48.test [14:44:47] [Load H1_n] Loading cached version of H1_n /project2/NextGenMapTest/Teaser/cache/dev_6846494ccbd564787b44a1791fba48ad.test [14:44:47] [Load H2_n] Loading cached version of H2_n /project2/NextGenMapTest/Teaser/cache/dev_80942a6e8ae85534a9a771eda3a94813.test [14:44:48] [Load D1_n] Loading cached version of D1_n /project2/NextGenMapTest/Teaser/cache/dev_e94bb6a8dc64c08d7513504925ee8f74.test [14:44:48] [Load M1_n] Loading cached version of M1_n /project2/NextGenMapTest/Teaser/cache/dev_714b3a538d57845a632effa7b54d3f72.test [14:44:48] [Load D2_n] Loading cached version of D2_n /project2/NextGenMapTest/Teaser/cache/dev_cba3bb381c26d4b6434e03d3576a0c27.test [14:44:48] [Load M2_n] Loading cached version of M2_n /project2/NextGenMapTest/Teaser/cache/dev_eb9fd06a04e8f26f66e8070da5e1beb1.test [14:44:48] [Load D3_n] Loading cached version of D3_n /project2/NextGenMapTest/Teaser/cache/dev_47238acfd6fea63728ca706247be351f.test [14:44:48] [Load M3_n] Loading cached version of M3_n /project2/NextGenMapTest/Teaser/cache/dev_7ab81d8343cecfe1a25eeca274864f06.test [14:44:48] [Load D4_n] Loading cached version of D4_n /project2/NextGenMapTest/Teaser/cache/dev_29911a054ddbec8763cca2c06361194d.test [14:44:48] [Load M4_n] Loading cached version of M4_n /project2/NextGenMapTest/Teaser/cache/dev_fef4bcb447b88ba596327064b14b8fd9.test [14:44:48] [Load H1_n] Loading cached version of H1_n /project2/NextGenMapTest/Teaser/cache/dev_d163f1c9e32b2e343f143d127e21a6ce.test [14:44:48] [Load H2_n] Loading cached version of H2_n /project2/NextGenMapTest/Teaser/cache/dev_96fc76414ade4a224349941a70b000ff.test [14:44:48] [Load D1_n] Loading cached version of D1_n /project2/NextGenMapTest/Teaser/cache/dev_3458b61afe71d5bf91bf0b8323270ac2.test [14:44:48] [Load M1_n] Loading cached version of M1_n /project2/NextGenMapTest/Teaser/cache/dev_873205e65ef7d14e43c21abd8e7bca94.test [14:44:48] [Load D2_n] Loading cached version of D2_n /project2/NextGenMapTest/Teaser/cache/dev_8515fcad20e39fcbc9b66549921c4abd.test [14:44:48] [Load M2_n] Loading cached version of M2_n /project2/NextGenMapTest/Teaser/cache/dev_54bb60b51e2daab49698e253a57e5cb0.test [14:44:48] [Load D3_n] Loading cached version of D3_n /project2/NextGenMapTest/Teaser/cache/dev_6563fb63a69496660c5faae654a66f12.test [14:44:48] [Load M3_n] Loading cached version of M3_n /project2/NextGenMapTest/Teaser/cache/dev_bf123ac423c801c7845526fcd107e312.test [14:44:48] [Load D4_n] Loading cached version of D4_n /project2/NextGenMapTest/Teaser/cache/dev_fc7bd99a9dd2a2a7c70464667e67b612.test [14:44:48] [Load H1_n] Loading cached version of H1_n /project2/NextGenMapTest/Teaser/cache/dev_5083237c418e4fd89d75515feaa5cf62.test [14:44:48] [Load H2_n] Loading cached version of H2_n /project2/NextGenMapTest/Teaser/cache/dev_bf9dd1542b5d3f28533e8cfcdf1d27b8.test [14:44:48] [Load D1_n] Loading cached version of D1_n /project2/NextGenMapTest/Teaser/cache/dev_26bba5ab17ce00cfe042e7d8722e27a4.test [14:44:48] [Load M1_n] Loading cached version of M1_n /project2/NextGenMapTest/Teaser/cache/dev_beba054056a8cd73f7f225fdb698c27e.test [14:44:48] [Load D2_n] Loading cached version of D2_n /project2/NextGenMapTest/Teaser/cache/dev_711cd2ae56f56faa5a4b2fb9078f2f24.test [14:44:48] [Load M2_n] Loading cached version of M2_n /project2/NextGenMapTest/Teaser/cache/dev_833a818e01da89308fbf921dbb4d5608.test [14:44:48] [Load D3_n] Loading cached version of D3_n /project2/NextGenMapTest/Teaser/cache/dev_3041c1ed97e9c14774f45371e6924e7b.test [14:44:48] [Load M3_n] Loading cached version of M3_n /project2/NextGenMapTest/Teaser/cache/dev_9f171f6e92bc973a9e5c8eac1a8b2487.test [14:44:48] [Load D4_n] Loading cached version of D4_n /project2/NextGenMapTest/Teaser/cache/dev_89dbc9af9112a0813886ca380a904c4f.test [14:44:48] [Load M4_n] Loading cached version of M4_n /project2/NextGenMapTest/Teaser/cache/dev_583b32ac04edf6bb969162405ac422f5.test [14:44:48] [Load H2_n] Loading cached version of H2_n /project2/NextGenMapTest/Teaser/cache/dev_64d740bb04c25be15637837ea386dfa2.test [14:44:49] [Load D1_n] Loading cached version of D1_n /project2/NextGenMapTest/Teaser/cache/dev_6f712d99f4b50df6e2bb85052a93d483.test [14:44:49] [Load M1_n] Loading cached version of M1_n /project2/NextGenMapTest/Teaser/cache/dev_44b45e80b4454fdf29d4f9bfdace85f2.test [14:44:49] [Load D2_n] Loading cached version of D2_n /project2/NextGenMapTest/Teaser/cache/dev_8c1827e66061f61af4bf0350199fc78d.test [14:44:49] [Load M2_n] Loading cached version of M2_n /project2/NextGenMapTest/Teaser/cache/dev_c025074cd59a1112db99aa5d91e4e07b.test [14:44:49] [Load D3_n] Loading cached version of D3_n /project2/NextGenMapTest/Teaser/cache/dev_54e7486693cdb8732e5f177a39b6b4f2.test [14:44:49] [Load M3_n] Loading cached version of M3_n /project2/NextGenMapTest/Teaser/cache/dev_c3f23b99409a67862f798bb6c33bc3d0.test [14:44:49] [Load D4_n] Loading cached version of D4_n /project2/NextGenMapTest/Teaser/cache/dev_c8db1fc40489f4f5b02603e2624b4f22.test [14:44:49] [Load M4_n] Loading cached version of M4_n /project2/NextGenMapTest/Teaser/cache/dev_8eb178d77998b1f96a9a57dbe125ffa9.test [14:44:49] [bowtie2 ] Skip: D1_n (already run) [14:44:49] [bowtie2 ] Skip: D2_n (already run) [14:44:49] [bowtie2 ] Skip: D3_n (already run) [14:44:49] [bowtie2 ] Skip: D4_n (already run) [14:44:49] [bowtie2 ] Skip: H1_n (already run) [14:44:49] [bowtie2 ] Skip: H2_n (already run) [14:44:49] [bowtie2 ] Skip: M1_n (already run) [14:44:49] [bowtie2 ] Skip: M2_n (already run) [14:44:49] [bowtie2 ] Skip: M3_n (already run) [14:44:49] [bowtie2 ] Skip: M4_n (already run) [14:44:49] [bwamem ] Skip: D1_n (already run) [14:44:49] [bwamem ] Skip: D2_n (already run) [14:44:49] [bwamem ] Skip: D3_n (already run) [14:44:49] [bwamem ] Skip: D4_n (already run) [14:44:49] [bwamem ] Skip: H1_n (already run) [14:44:49] [bwamem ] Skip: H2_n (already run) [14:44:49] [bwamem ] Skip: M1_n (already run) [14:44:49] [bwamem ] Skip: M2_n (already run) [14:44:49] [bwamem ] Skip: M3_n (already run) [14:44:49] [bwamem ] M4_n (base: tests_base/base_mapping) [14:44:49] [init ] Ref: /project2/NextGenMapTest/Teaser/references/m_musculus.fasta [14:44:49] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/M4_n/reads.fastq [14:44:49] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/M4_n/out_bwamem.sam [14:44:49] [map ] Command(pre): [14:44:49] [map ] Base run time file not existing, performing base run [14:44:49] [map ] Command(pre-b): /project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwamem.sam [14:46:55] [map ] Command(main): /project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads.fastq -t 4 > out_bwamem.sam [14:46:55] [map ] Mapping 140.00MB to 4919.00MB with bwamem... [14:49:30] [map ] Took 154.433 (wall), 478.482 (CPU) seconds, initialization time: 24.258 (wall), 2.345 (CPU) seconds. [14:49:30] [map ] Command(post): [14:49:30] [sort_prepare] Sorting... [14:49:30] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [14:49:57] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 0,0,0,2199284,0,2199284,0,0,0,0,0 [14:49:57] [calc_stats ] Unexpectedly reached end of mapper output at sorted_out_bwamem.sam:read.000000000 [14:49:57] [calc_stats ] None [14:49:58] [bwamem ] Errors in test, not caching! [14:49:58] [bwa ] Skip: D1_n (already run) [14:49:58] [bwa ] Skip: D2_n (already run) [14:49:58] [bwa ] Skip: D3_n (already run) [14:49:58] [bwa ] Skip: D4_n (already run) [14:49:58] [bwa ] Skip: H1_n (already run) [14:49:58] [bwa ] Skip: H2_n (already run) [14:49:58] [bwa ] Skip: M1_n (already run) [14:49:58] [bwa ] Skip: M2_n (already run) [14:49:58] [bwa ] Skip: M3_n (already run) [14:49:58] [bwa ] Skip: M4_n (already run) [14:49:58] [bwasw ] Skip: D1_n (already run) [14:49:58] [bwasw ] Skip: D2_n (already run) [14:49:58] [bwasw ] Skip: D3_n (already run) [14:49:58] [bwasw ] Skip: D4_n (already run) [14:49:58] [bwasw ] Skip: H1_n (already run) [14:49:58] [bwasw ] Skip: H2_n (already run) [14:49:58] [bwasw ] Skip: M1_n (already run) [14:49:58] [bwasw ] Skip: M2_n (already run) [14:49:58] [bwasw ] Skip: M3_n (already run) [14:49:58] [bwasw ] M4_n (base: tests_base/base_mapping) [14:49:58] [init ] Ref: /project2/NextGenMapTest/Teaser/references/m_musculus.fasta [14:49:58] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/M4_n/reads.fastq [14:49:58] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/M4_n/out_bwasw.sam [14:49:58] [map ] Command(pre): [14:49:58] [map ] Base run time file not existing, performing base run [14:49:58] [map ] Command(pre-b): /project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam [14:51:40] [map ] Command(main): /project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/m_musculus.fasta reads.fastq -t 4 > out_bwasw.sam [14:51:40] [map ] Mapping 140.00MB to 4919.00MB with bwasw... [14:51:52] [map ] Took 11.824 (wall), 6.505 (CPU) seconds, initialization time: 11.707 (wall), 2.307 (CPU) seconds. [14:51:52] [map ] Command(post): [14:51:52] [sort_prepare] Sorting... [14:52:00] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [14:52:37] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 0,0,2199284,0,0,2199284,0,0,0,0,0 [14:52:38] [ngm-0.4.13 ] Skip: D1_n (already run) [14:52:38] [ngm-0.4.13 ] Skip: D2_n (already run) [14:52:38] [ngm-0.4.13 ] Skip: D3_n (already run) [14:52:38] [ngm-0.4.13 ] Skip: D4_n (already run) [14:52:38] [ngm-0.4.13 ] Skip: H1_n (already run) [14:52:38] [ngm-0.4.13 ] Skip: H2_n (already run) [14:52:38] [ngm-0.4.13 ] Skip: M1_n (already run) [14:52:38] [ngm-0.4.13 ] Skip: M2_n (already run) [14:52:38] [ngm-0.4.13 ] Skip: M3_n (already run) [14:52:38] [ngm-0.4.13 ] Skip: M4_n (already run) [14:52:38] [ngm-0.5.2 ] Skip: D1_n (already run) [14:52:38] [ngm-0.5.2 ] Skip: D2_n (already run) [14:52:38] [ngm-0.5.2 ] Skip: D3_n (already run) [14:52:38] [ngm-0.5.2 ] Skip: D4_n (already run) [14:52:38] [ngm-0.5.2 ] H1_n (base: tests_base/base_mapping) [14:52:38] [init ] Ref: /project2/NextGenMapTest/Teaser/references/GRCh37.fa [14:52:38] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/H1_n/reads1.fastq [14:52:38] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/H1_n/out_ngm-0.5.2.sam [14:52:38] [map ] Command(pre): [14:52:38] [map ] Base run time file not existing, performing base run [14:52:38] [map ] Command(pre-b): /software/ngm/dev/ngm-0.5.2/ngm --output out_ngm-0.5.2.sam --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --qry reads_base.fastq --no-progress [14:53:41] [map ] Command(main): /software/ngm/dev/ngm-0.5.2/ngm --qry2 reads2.fastq --output out_ngm-0.5.2.sam --qry1 reads1.fastq --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --no-progress [14:53:41] [map ] Mapping 86.00MB to 3199.00MB with ngm-0.5.2... [14:54:04] [map ] Took 22.279 (wall), 62.610 (CPU) seconds, initialization time: 2.504 (wall), 2.456 (CPU) seconds. [14:54:04] [map ] Command(post): [14:54:05] [sort_prepare] Sorting... [14:54:08] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [14:54:15] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 299502,13892,318,0,4,313712,0,0,0.955672412363,0.998939363618,0.976827013082 [14:54:15] [ngm-0.5.2 ] Skip: H2_n (already run) [14:54:15] [ngm-0.5.2 ] Skip: M1_n (already run) [14:54:15] [ngm-0.5.2 ] Skip: M2_n (already run) [14:54:15] [ngm-0.5.2 ] Skip: M3_n (already run) [14:54:15] [ngm-0.5.2 ] Skip: M4_n (already run) [14:54:15] [ngm-0.5.3 ] D1_n (base: tests_base/base_mapping) [14:54:15] [init ] Ref: /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta [14:54:15] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/D1_n/reads.fastq [14:54:15] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/D1_n/out_ngm-0.5.3.sam [14:54:15] [map ] Command(pre): [14:54:15] [map ] Base run time file not existing, performing base run [14:54:15] [map ] Command(pre-b): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress [14:54:25] [map ] Command(main): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads.fastq --no-progress [14:54:25] [map ] Mapping 76.00MB to 146.00MB with ngm-0.5.3... [14:54:35] [map ] Took 9.400 (wall), 26.754 (CPU) seconds, initialization time: 1.346 (wall), 1.442 (CPU) seconds. [14:54:35] [map ] Command(post): [14:54:35] [sort_prepare] Sorting... [14:54:37] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [14:54:45] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 219322,20172,49,0,0,239543,0,0,0.915772420186,0.999776634104,0.955932572761 [14:54:45] [ngm-0.5.3 ] D2_n (base: tests_base/base_mapping) [14:54:45] [init ] Ref: /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta [14:54:45] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/D2_n/reads.fastq [14:54:45] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/D2_n/out_ngm-0.5.3.sam [14:54:45] [map ] Command(pre): [14:54:45] [map ] Base run time file not existing, performing base run [14:54:45] [map ] Command(pre-b): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress [14:54:49] [map ] Command(main): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads.fastq --no-progress [14:54:49] [map ] Mapping 76.00MB to 146.00MB with ngm-0.5.3... [14:55:01] [map ] Took 11.999 (wall), 31.171 (CPU) seconds, initialization time: 1.451 (wall), 1.440 (CPU) seconds. [14:55:01] [map ] Command(post): [14:55:02] [sort_prepare] Sorting... [14:55:04] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [14:55:17] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 219501,20027,15,0,0,239543,0,0,0.916389733142,0.999931667851,0.956339697284 [14:55:18] [ngm-0.5.3 ] D3_n (base: tests_base/base_mapping) [14:55:18] [init ] Ref: /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta [14:55:18] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/D3_n/reads.fastq [14:55:18] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/D3_n/out_ngm-0.5.3.sam [14:55:18] [map ] Command(pre): [14:55:18] [map ] Base run time file not existing, performing base run [14:55:18] [map ] Command(pre-b): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress [14:55:22] [map ] Command(main): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads.fastq --no-progress [14:55:22] [map ] Mapping 88.00MB to 146.00MB with ngm-0.5.3... [14:55:46] [map ] Took 23.715 (wall), 76.903 (CPU) seconds, initialization time: 1.277 (wall), 1.433 (CPU) seconds. [14:55:46] [map ] Command(post): [14:55:46] [sort_prepare] Sorting... [14:55:49] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [14:55:53] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 165885,13762,10,0,0,179657,0,0,0.923394211982,0.999939720908,0.960143774129 [14:55:53] [ngm-0.5.3 ] D4_n (base: tests_base/base_mapping) [14:55:53] [init ] Ref: /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta [14:55:53] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/D4_n/reads.fastq [14:55:53] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/D4_n/out_ngm-0.5.3.sam [14:55:53] [map ] Command(pre): [14:55:53] [map ] Base run time file not existing, performing base run [14:55:53] [map ] Command(pre-b): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads_base.fastq --no-progress [14:55:57] [map ] Command(main): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/d_melanogaster.fasta -t 4 --qry reads.fastq --no-progress [14:55:57] [map ] Mapping 104.00MB to 146.00MB with ngm-0.5.3... [14:56:09] [map ] Took 11.278 (wall), 26.180 (CPU) seconds, initialization time: 1.268 (wall), 1.426 (CPU) seconds. [14:56:09] [map ] Command(post): [14:56:09] [sort_prepare] Sorting... [14:56:18] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [14:56:55] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 1319097,297403,16749,0,0,1633249,4,0,0.816020414476,0.987461878091,0.893592417691 [14:56:55] [ngm-0.5.3 ] H1_n (base: tests_base/base_mapping) [14:56:55] [init ] Ref: /project2/NextGenMapTest/Teaser/references/GRCh37.fa [14:56:55] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/H1_n/reads1.fastq [14:56:55] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/H1_n/out_ngm-0.5.3.sam [14:56:55] [map ] Command(pre): [14:56:55] [map ] Base run time file not existing, performing base run [14:56:55] [map ] Command(pre-b): /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 [14:57:03] [map ] Command(main): /software/ngm/dev/ngm-0.5.3/ngm --qry2 reads2.fastq --output out_ngm-0.5.3.sam --qry1 reads1.fastq --ref /project2/NextGenMapTest/Teaser/references/GRCh37.fa -t 4 --no-progress [14:57:03] [map ] Mapping 86.00MB to 3199.00MB with ngm-0.5.3... [14:57:26] [map ] Took 22.337 (wall), 64.816 (CPU) seconds, initialization time: 2.618 (wall), 3.004 (CPU) seconds. [14:57:26] [map ] Command(post): [14:57:26] [sort_prepare] Sorting... [14:57:30] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [14:57:36] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 299502,13892,318,0,4,313712,0,0,0.955672412363,0.998939363618,0.976827013082 [14:57:36] [ngm-0.5.3 ] H2_n (base: tests_base/base_mapping) [14:57:36] [init ] Ref: /project2/NextGenMapTest/Teaser/references/GRCh37.fa [14:57:36] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/H2_n/reads.fastq [14:57:36] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/H2_n/out_ngm-0.5.3.sam [14:57:36] [map ] Command(pre): [14:57:36] [map ] Base run time file not existing, performing base run [14:57:36] [map ] Command(pre-b): /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 [14:57:43] [map ] Command(main): /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 [14:57:43] [map ] Mapping 82.00MB to 3199.00MB with ngm-0.5.3... [14:58:05] [map ] Took 21.479 (wall), 64.046 (CPU) seconds, initialization time: 2.307 (wall), 2.366 (CPU) seconds. [14:58:05] [map ] Command(post): [14:58:05] [sort_prepare] Sorting... [14:58:08] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [14:58:14] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 297625,15782,306,0,3,313713,0,0,0.949643753968,0.998972916548,0.973683952249 [14:58:15] [ngm-0.5.3 ] M1_n (base: tests_base/base_mapping) [14:58:15] [init ] Ref: /project2/NextGenMapTest/Teaser/references/m_musculus.fasta [14:58:15] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/M1_n/reads.fastq [14:58:15] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/M1_n/out_ngm-0.5.3.sam [14:58:15] [map ] Command(pre): [14:58:15] [map ] Base run time file not existing, performing base run [14:58:15] [map ] Command(pre-b): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads_base.fastq --no-progress [15:00:30] [map ] Command(main): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads.fastq --no-progress [15:00:30] [map ] Mapping 103.00MB to 4919.00MB with ngm-0.5.3... [15:01:45] [map ] Took 74.205 (wall), 136.386 (CPU) seconds, initialization time: 64.732 (wall), 10.425 (CPU) seconds. [15:01:45] [map ] Command(post): [15:01:45] [sort_prepare] Sorting... [15:01:48] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [15:01:58] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 300743,20694,1124,0,0,322561,0,0,0.935620354844,0.996276505878,0.964996213726 [15:01:58] [ngm-0.5.3 ] M2_n (base: tests_base/base_mapping) [15:01:58] [init ] Ref: /project2/NextGenMapTest/Teaser/references/m_musculus.fasta [15:01:58] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/M2_n/reads.fastq [15:01:58] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/M2_n/out_ngm-0.5.3.sam [15:01:59] [map ] Command(pre): [15:01:59] [map ] Base run time file not existing, performing base run [15:01:59] [map ] Command(pre-b): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads_base.fastq --no-progress [15:02:32] [map ] Command(main): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads.fastq --no-progress [15:02:32] [map ] Mapping 103.00MB to 4919.00MB with ngm-0.5.3... [15:03:31] [map ] Took 58.129 (wall), 203.692 (CPU) seconds, initialization time: 3.402 (wall), 3.847 (CPU) seconds. [15:03:31] [map ] Command(post): [15:03:31] [sort_prepare] Sorting... [15:03:34] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [15:03:52] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 296292,26235,34,0,0,322561,0,0,0.918657972821,0.999885261503,0.957552116577 [15:03:52] [ngm-0.5.3 ] M3_n (base: tests_base/base_mapping) [15:03:52] [init ] Ref: /project2/NextGenMapTest/Teaser/references/m_musculus.fasta [15:03:52] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/M3_n/reads.fastq [15:03:52] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/M3_n/out_ngm-0.5.3.sam [15:03:52] [map ] Command(pre): [15:03:52] [map ] Base run time file not existing, performing base run [15:03:52] [map ] Command(pre-b): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads_base.fastq --no-progress [15:03:58] [map ] Command(main): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads.fastq --no-progress [15:03:58] [map ] Mapping 119.00MB to 4919.00MB with ngm-0.5.3... [15:09:56] [map ] Took 356.345 (wall), 1334.065 (CPU) seconds, initialization time: 2.511 (wall), 2.643 (CPU) seconds. [15:09:56] [map ] Command(post): [15:09:56] [sort_prepare] Sorting... [15:10:00] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [15:10:06] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 226154,15749,18,0,0,241921,0,0,0.934895391955,0.999920414552,0.966315227261 [15:10:06] [ngm-0.5.3 ] M4_n (base: tests_base/base_mapping) [15:10:06] [init ] Ref: /project2/NextGenMapTest/Teaser/references/m_musculus.fasta [15:10:06] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/M4_n/reads.fastq [15:10:06] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/M4_n/out_ngm-0.5.3.sam [15:10:06] [map ] Command(pre): [15:10:06] [map ] Base run time file not existing, performing base run [15:10:06] [map ] Command(pre-b): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads_base.fastq --no-progress [15:10:12] [map ] Command(main): /software/ngm/dev/ngm-0.5.3/ngm --output out_ngm-0.5.3.sam --ref /project2/NextGenMapTest/Teaser/references/m_musculus.fasta -t 4 --qry reads.fastq --no-progress [15:10:12] [map ] Mapping 140.00MB to 4919.00MB with ngm-0.5.3... [15:10:47] [map ] Took 34.356 (wall), 107.280 (CPU) seconds, initialization time: 2.462 (wall), 2.640 (CPU) seconds. [15:10:47] [map ] Command(post): [15:10:47] [sort_prepare] Sorting... [15:10:58] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 50)... [15:11:48] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 1567393,489535,142356,0,0,2199284,10,0,0.762006740148,0.916738655791,0.832241787655