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 '997fdd990ed1fa021b2dc57eaab6d9c9' due to an exception: [Errno 2] No such file or directory: u'/project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq'
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 Accession997fdd990ed1fa021b2dc57eaab6d9c9
Report timestampWed May 17 23:36:40 2017
Framework Version1.2-public-vevev
Framework Working Directory/project/teaser/genometeaser/tests_generated/997fdd990ed1fa021b2dc57eaab6d9c9
Framework Command Line./teaser.py setups_generated/997fdd990ed1fa021b2dc57eaab6d9c9.yaml -mcpu
Benchmark Configuration
evaluation: {pos_threshold: 30}
include: [base_teaser.yaml]
meta_timestamp: 1495056526.431652
report: {name: 997fdd990ed1fa021b2dc57eaab6d9c9}
sub_max_memory: 14000
sub_max_runtime: 900
teaser:
  tests:
    997fdd990ed1fa021b2dc57eaab6d9c9: {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/997fdd990ed1fa021b2dc57eaab6d9c9.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 997fdd990ed1fa021b2dc57eaab6d9c9
[23:32:37] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/997fdd990ed1fa021b2dc57eaab6d9c9
[23:32:37] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/997fdd990ed1fa021b2dc57eaab6d9c9
[23:32:37] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[23:32:37] [Teaser      ] csample /project/teaser/genometeaser/references/D_melanogaster.fasta 600 0.250000
[23:32:37] [Teaser      ] Loaded index from /project/teaser/genometeaser/references/D_melanogaster.fasta.teaser.findex
[23:32:37] [Teaser      ] Sampling as contig: 59885 regions of size 600 (pad 120), totalling 35931498 base pairs
[23:32:37] [Teaser      ] Sampling 59885 regions
[23:33:00] [Teaser      ] 10%
[23:33:16] [Teaser      ] 20%
[23:33:26] [Teaser      ] 30%
[23:33:40] [Teaser      ] 40%
[23:33:49] [Teaser      ] 50%
[23:34:01] [Teaser      ] 60%
[23:34:17] [Teaser      ] 70%
[23:34:34] [Teaser      ] 80%
[23:34:51] [Teaser      ] 90%
[23:35:04] [Teaser      ] 100%
[23:35:05] [Teaser      ] change directory /project/teaser/genometeaser/tests_generated/997fdd990ed1fa021b2dc57eaab6d9c9
[23:35:05] [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
[23:35:05] [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
[23:36:39] [Teaser      ] move /project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq -> ./reads.fastq
[23:36:39] [Teaser      ] Teaser: Test creation failed for '997fdd990ed1fa021b2dc57eaab6d9c9' due to an exception: [Errno 2] No such file or directory: u'/project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq'
[23:36:40] [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 260, in makeDatasetDS
    self.simulate(test)
  File "/project/teaser/genometeaser/lib/teaser.py", line 463, in simulate
    sim.simulate()
  File "/project/teaser/genometeaser/lib/simulator.py", line 84, in simulate
    self.mv(self.dataset["reference_sim"] + ".fastq", "./reads.fastq")
  File "/project/teaser/genometeaser/lib/simulator.py", line 35, in mv
    shutil.move(a, b)
  File "/project/teaser/miniconda2/lib/python2.7/shutil.py", line 302, in move
    copy2(src, real_dst)
  File "/project/teaser/miniconda2/lib/python2.7/shutil.py", line 130, in copy2
    copyfile(src, dst)
  File "/project/teaser/miniconda2/lib/python2.7/shutil.py", line 82, in copyfile
    with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: u'/project/teaser/genometeaser/references/D_melanogaster.fasta.sampled.4.600.120.fasta.fastq'

[23:36:40] [ReportGen   ] This benchmark contains no tests. This could be because no tests or mappers were selected, or because generation/loading failed for all tests.