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.

0 tests executed, 0 fail, 0 aborted, 0 errors total.
StateNameReferenceExecutedOKWarningsErrors
Errors and Warnings
TypeMessage
This benchmark contains no tests. This could be because no tests or mappers were selected, or because generation/loading failed for all tests.
Teaser: Test creation failed for '57a0e142492953639f1b7934d38bae70' due to an exception: No JSON object could be decoded
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 Accession57a0e142492953639f1b7934d38bae70
Report timestampWed May 17 23:35:05 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser/tests_generated/57a0e142492953639f1b7934d38bae70
Framework Command Line./teaser.py setups_generated/57a0e142492953639f1b7934d38bae70.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1495056514.42641
report: {name: 57a0e142492953639f1b7934d38bae70}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    57a0e142492953639f1b7934d38bae70: {coverage: 1.0, error_rate_mult: 1.0, mutation_indel_avg_len: 1.0,
      mutation_indel_frac: 0.3, mutation_rate: 0.01, paired: false, platform: !!python/unicode 'illumina',
      read_length: 60, reference: !!python/unicode 'D_melanogaster.fasta', title: !!python/unicode 'D_melanogaster',
      type: !!python/unicode 'simulated_teaser'}
test_mappers: [bowtie2, bwa, bwamem, bwasw, ngm]
test_parameters: []
threads: 4
Log
[23:32:36] [Main        ] framework cmd:  ./teaser.py setups_generated/57a0e142492953639f1b7934d38bae70.yaml -mcpu
[23:32:36] [Main        ] framework hash: vevev
[23:32:36] [Main        ] deployment mode: devel (True)
[23:32:36] [Main        ] Test Runner Setup - ""

[23:32:37] [Main        ] Using Teaser for data set creation
[23:32:37] [Teaser      ] Init. Creating 1 test datasets.
[23:32:37] [Teaser      ] 
[23:32:37] [Teaser      ] Creating test 57a0e142492953639f1b7934d38bae70
[23:32:38] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/57a0e142492953639f1b7934d38bae70
[23:32:38] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/57a0e142492953639f1b7934d38bae70
[23:32:38] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[23:32:38] [Teaser      ] csample /project/teaser/genometeaser/references/D_melanogaster.fasta 600 0.250000
[23:32:38] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[23:32:38] [Teaser      ] Sampling as contig: 59885 regions of size 600 (pad 120), totalling 35931498 base pairs
[23:32:38] [Teaser      ] Sampling 59885 regions
[23:33:06] [Teaser      ] 10%
[23:33:21] [Teaser      ] 20%
[23:33:29] [Teaser      ] 30%
[23:33:34] [Teaser      ] 40%
[23:33:39] [Teaser      ] 50%
[23:33:45] [Teaser      ] 60%
[23:33:50] [Teaser      ] 70%
[23:33:55] [Teaser      ] 80%
[23:34:00] [Teaser      ] 90%
[23:34:05] [Teaser      ] 100%
[23:34:06] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/57a0e142492953639f1b7934d38bae70
[23:34:06] [Teaser      ] 	Simulator cmd: /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 598858  --ll 500 --le 50  --hi 0.003000  --hs 0.007000  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta
[23:34:06] [Teaser      ] subprogram /project/teaser/genometeaser/software/mason illumina --read-name-prefix read --sq -n 60 -N 598858  --ll 500 --le 50  --hi 0.003000  --hs 0.007000  --hm 1 --hM 4 --source-no-N  /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta
[23:35:04] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq -> ./reads.fastq
[23:35:04] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq.sam -> ./mapping_comparison.sam
[23:35:04] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/57a0e142492953639f1b7934d38bae70
[23:35:04] [Teaser      ] move mapping_comparison.sam -> mapping_comparison_unfixed.sam
[23:35:04] [Teaser      ] Translating SAM file coordinates (as contig)...
[23:35:04] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[23:35:04] [Teaser      ] Teaser: Test creation failed for '57a0e142492953639f1b7934d38bae70' due to an exception: No JSON object could be decoded
[23:35:05] [Teaser      ] Teaser Error, exception: Traceback (most recent call last):
  File "/project/teaser/genometeaser/lib/teaser.py", line 134, in createTest
    self.makeDatasetDS(test)
  File "/project/teaser/genometeaser/lib/teaser.py", line 264, in makeDatasetDS
    gsample.ctranslate(test["reference"], sampled_index_file, "mapping_comparison_unfixed.sam", "mapping_comparison.sam",self.config["fastindex_path"])
  File "/project/teaser/genometeaser/lib/gsample.py", line 262, in ctranslate
    sampled_idx = json.loads(open(sampled_index_file, "r").read())
  File "/project/teaser/miniconda2/lib/python2.7/json/__init__.py", line 339, in loads
    return _default_decoder.decode(s)
  File "/project/teaser/miniconda2/lib/python2.7/json/decoder.py", line 364, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/project/teaser/miniconda2/lib/python2.7/json/decoder.py", line 382, in raw_decode
    raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded

[23:35:05] [ReportGen   ] This benchmark contains no tests. This could be because no tests or mappers were selected, or because generation/loading failed for all tests.