Tests Overview
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.
5 tests executed, 0 fail, 0 aborted, 0 errors total.| State | Name | Reference | Executed | OK | Warnings | Errors |
|---|---|---|---|---|---|---|
| ecoli_test | E_coli | 5 | 5 | 0 | 0 |
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 | example_ecoli |
|---|---|
| Report timestamp | Fri Jan 20 17:33:40 2017 |
| Framework Version | 1.2-public-vevev | Framework Working Directory | /project2/NextGenMapTest/Teaser |
| Framework Command Line | ./teaser.py -tc 4 setups/example_ecoli.yaml |
| Benchmark Configuration | |
evaluation: {pos_threshold: 10}
include: [base_teaser.yaml]
report: {directory: /home/CIBIV/philipp_/public_html/teaser/report, name: example_ecoli}
teaser:
tests:
ecoli_test: {reference: E_coli.fasta}
threads: 1
| |
Log
[17:31:49] [Main ] framework cmd: ./teaser.py -tc 4 setups/example_ecoli.yaml [17:31:49] [Main ] framework hash: vevev [17:31:49] [Main ] deployment mode: production (False) [17:31:49] [Main ] Test Runner Setup - "" [17:31:49] [Main ] Using Teaser for data set creation [17:31:49] [Teaser ] Init. Creating 1 test datasets. [17:31:49] [Teaser ] [17:31:49] [Teaser ] Creating test ecoli_test [17:31:49] [Teaser ] change directory /project2/NextGenMapTest/Teaser/tests_generated/ecoli_test [17:31:49] [Teaser ] change directory /project2/NextGenMapTest/Teaser/tests_generated/ecoli_test [17:31:49] [Teaser ] Indexing /project2/NextGenMapTest/Teaser/references/E_coli.fasta [17:31:50] [Teaser ] csample /project2/NextGenMapTest/Teaser/references/E_coli.fasta 1000 0.500000 [17:31:50] [Teaser ] Loaded index from /project2/NextGenMapTest/Teaser/references/E_coli.fasta.teaser.findex [17:31:50] [Teaser ] Sampling as contig: 2566 regions of size 1000 (pad 200), totalling 2566034 base pairs [17:31:50] [Teaser ] Sampling 2566 regions [17:31:50] [Teaser ] 10% [17:31:50] [Teaser ] 20% [17:31:50] [Teaser ] 30% [17:31:50] [Teaser ] 40% [17:31:50] [Teaser ] 50% [17:31:50] [Teaser ] 60% [17:31:50] [Teaser ] 70% [17:31:50] [Teaser ] 80% [17:31:50] [Teaser ] 90% [17:31:50] [Teaser ] 100% [17:31:50] [Teaser ] change directory /project2/NextGenMapTest/Teaser/tests_generated/ecoli_test [17:31:50] [Teaser ] Simulator cmd: /project2/NextGenMapTest/Teaser/software/mason illumina --read-name-prefix read --sq -n 100 -N 150000 --ll 500 --le 50 --hi 0.000300 --hs 0.000700 --hm 1 --hM 4 /project2/NextGenMapTest/Teaser/references/E_coli.fasta.sampled.2.1000.200.fasta [17:31:50] [Teaser ] subprogram /project2/NextGenMapTest/Teaser/software/mason illumina --read-name-prefix read --sq -n 100 -N 150000 --ll 500 --le 50 --hi 0.000300 --hs 0.000700 --hm 1 --hM 4 /project2/NextGenMapTest/Teaser/references/E_coli.fasta.sampled.2.1000.200.fasta [17:32:10] [Teaser ] move /project2/NextGenMapTest/Teaser/references/E_coli.fasta.sampled.2.1000.200.fasta.fastq -> ./reads.fastq [17:32:10] [Teaser ] move /project2/NextGenMapTest/Teaser/references/E_coli.fasta.sampled.2.1000.200.fasta.fastq.sam -> ./mapping_comparison.sam [17:32:10] [Teaser ] change directory /project2/NextGenMapTest/Teaser/tests_generated/ecoli_test [17:32:10] [Teaser ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam [17:32:10] [Teaser ] Translating SAM file coordinates (as contig)... [17:32:10] [Teaser ] Loaded index from /project2/NextGenMapTest/Teaser/references/E_coli.fasta.teaser.findex [17:32:16] [Teaser ] remove /project2/NextGenMapTest/Teaser/references/E_coli.fasta.sampled.2.1000.200.fasta [17:32:16] [Teaser ] remove /project2/NextGenMapTest/Teaser/references/E_coli.fasta.sampled.2.1000.200.fasta.index [17:32:16] [Teaser ] remove mapping_comparison_unfixed.sam [17:32:16] [Teaser ] Took 26 seconds for generating ecoli_test [17:32:16] [Main ] Data set creation completed [17:32:16] [Main ] [17:32:16] [bowtie2 ] ecoli_test (base: tests_base/base_mapping) [17:32:16] [init ] Ref: /project2/NextGenMapTest/Teaser/references/E_coli.fasta [17:32:16] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/ecoli_test/reads.fastq [17:32:16] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test/out_bowtie2.sam [17:32:16] [map ] Command(pre): /project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2-build /project2/NextGenMapTest/Teaser/references/E_coli.fasta /project2/NextGenMapTest/Teaser/references/E_coli.fasta_bt [17:32:22] [map ] Base run time file not existing, performing base run [17:32:22] [map ] Command(pre-b): /project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/E_coli.fasta_bt -U reads_base.fastq -S out_bowtie2.sam [17:32:24] [map ] Command(main): /project2/NextGenMapTest/Teaser/software/bowtie2/bowtie2 -p 4 -x /project2/NextGenMapTest/Teaser/references/E_coli.fasta_bt -U reads.fastq -S out_bowtie2.sam [17:32:24] [map ] Mapping 33.00MB to 5.00MB with bowtie2... [17:32:28] [map ] Took 3.402 (wall), 10.479 (CPU) seconds, initialization time: 0.164 (wall), 0.144 (CPU) seconds. [17:32:28] [map ] Command(post): [17:32:28] [sort_prepare] Sorting... [17:32:30] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 10)... [17:32:35] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 144458,5536,6,0,0,150000,0,0,0.963091857008,0.999958467161,0.981178979685 [17:32:35] [bwa ] ecoli_test (base: tests_base/base_mapping) [17:32:35] [init ] Ref: /project2/NextGenMapTest/Teaser/references/E_coli.fasta [17:32:35] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/ecoli_test/reads.fastq [17:32:35] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test/out_bwa.sam [17:32:35] [map ] Command(pre): /project2/NextGenMapTest/Teaser/software/bwa index /project2/NextGenMapTest/Teaser/references/E_coli.fasta [17:32:37] [map ] Base run time file not existing, performing base run [17:32:37] [map ] Command(pre-b): /project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/E_coli.fasta out_bwa.sam.bwa reads_base.fastq > out_bwa.sam [17:32:39] [map ] Command(main): /project2/NextGenMapTest/Teaser/software/bwa aln /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads.fastq -t 4 > out_bwa.sam.bwa; /project2/NextGenMapTest/Teaser/software/bwa samse /project2/NextGenMapTest/Teaser/references/E_coli.fasta out_bwa.sam.bwa reads.fastq > out_bwa.sam [17:32:39] [map ] Mapping 33.00MB to 5.00MB with bwa... [17:32:44] [map ] Took 4.345 (wall), 8.990 (CPU) seconds, initialization time: 0.040 (wall), 0.017 (CPU) seconds. [17:32:44] [map ] Command(post): [17:32:44] [sort_prepare] Sorting... [17:32:45] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 10)... [17:32:49] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 141813,5357,2830,0,0,150000,0,0,0.963599918462,0.980434587225,0.971944361629 [17:32:49] [bwamem ] ecoli_test (base: tests_base/base_mapping) [17:32:49] [init ] Ref: /project2/NextGenMapTest/Teaser/references/E_coli.fasta [17:32:49] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/ecoli_test/reads.fastq [17:32:49] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test/out_bwamem.sam [17:32:49] [map ] Command(pre): [17:32:49] [map ] Base run time file not existing, performing base run [17:32:49] [map ] Command(pre-b): /project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwamem.sam [17:32:51] [map ] Command(main): /project2/NextGenMapTest/Teaser/software/bwa mem /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads.fastq -t 4 > out_bwamem.sam [17:32:51] [map ] Mapping 33.00MB to 5.00MB with bwamem... [17:32:54] [map ] Took 2.460 (wall), 6.723 (CPU) seconds, initialization time: 0.015 (wall), 0.011 (CPU) seconds. [17:32:54] [map ] Command(post): [17:32:54] [sort_prepare] Sorting... [17:32:56] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 10)... [17:33:00] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 144443,5557,0,0,0,150000,0,0,0.962953333333,1.0,0.981127077227 [17:33:00] [bwasw ] ecoli_test (base: tests_base/base_mapping) [17:33:00] [init ] Ref: /project2/NextGenMapTest/Teaser/references/E_coli.fasta [17:33:00] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/ecoli_test/reads.fastq [17:33:00] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test/out_bwasw.sam [17:33:00] [map ] Command(pre): [17:33:00] [map ] Base run time file not existing, performing base run [17:33:00] [map ] Command(pre-b): /project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads_base.fastq -t 4 > out_bwasw.sam [17:33:02] [map ] Command(main): /project2/NextGenMapTest/Teaser/software/bwa bwasw /project2/NextGenMapTest/Teaser/references/E_coli.fasta reads.fastq -t 4 > out_bwasw.sam [17:33:02] [map ] Mapping 33.00MB to 5.00MB with bwasw... [17:33:14] [map ] Took 11.775 (wall), 43.957 (CPU) seconds, initialization time: 0.195 (wall), 0.014 (CPU) seconds. [17:33:14] [map ] Command(post): [17:33:14] [sort_prepare] Sorting... [17:33:15] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 10)... [17:33:19] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 144336,5627,37,0,4,150000,0,0,0.962477411095,0.999743719394,0.980756686236 [17:33:19] [ngm ] ecoli_test (base: tests_base/base_mapping) [17:33:19] [init ] Ref: /project2/NextGenMapTest/Teaser/references/E_coli.fasta [17:33:19] [init ] Reads: /project2/NextGenMapTest/Teaser/tests_generated/ecoli_test/reads.fastq [17:33:19] [init ] Output:/project2/NextGenMapTest/Teaser/tests_generated/ecoli_test/out_ngm.sam [17:33:19] [map ] Command(pre): /project2/NextGenMapTest/Teaser/software/ngm/ngm --ref /project2/NextGenMapTest/Teaser/references/E_coli.fasta [17:33:27] [map ] Base run time file not existing, performing base run [17:33:27] [map ] Command(pre-b): /project2/NextGenMapTest/Teaser/software/ngm/ngm --output out_ngm.sam --ref /project2/NextGenMapTest/Teaser/references/E_coli.fasta -t 4 --qry reads_base.fastq --no-progress [17:33:31] [map ] Command(main): /project2/NextGenMapTest/Teaser/software/ngm/ngm --output out_ngm.sam --ref /project2/NextGenMapTest/Teaser/references/E_coli.fasta -t 4 --qry reads.fastq --no-progress [17:33:31] [map ] Mapping 33.00MB to 5.00MB with ngm... [17:33:35] [map ] Took 3.475 (wall), 7.964 (CPU) seconds, initialization time: 1.112 (wall), 1.239 (CPU) seconds. [17:33:35] [map ] Command(post): [17:33:35] [sort_prepare] Sorting... [17:33:36] [calc_stats ] Compute mapping statistics (lib.evaluator.ThresholdBasedEvaluator, threshold 10)... [17:33:40] [calc_stats ] correct,wrong,not_mapped,not_found,not_found_comparison,total,reverse,secondary,precision,recall,fmeasure 144448,5552,0,0,0,150000,0,0,0.962986666667,1.0,0.981144378634