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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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error in funannotate test #393

Closed Homap closed 3 years ago

Homap commented 4 years ago

Hello,

Trying to run funannotate test -t all --cpus 8, I get the following error: 

#########################################################
Running `funannotate clean` unit testing: minimap2 mediated assembly duplications
CMD: funannotate clean -i test.clean.fa -o test.exhaustive.fa --exhaustive
#########################################################
-----------------------------------------------
6 input contigs, 6 larger than 500 bp, N50 is 427,039 bp
Checking duplication of 6 contigs
-----------------------------------------------
scaffold_91 appears duplicated: 100% identity over 100% of the contig. contig length: 8858
scaffold_73 appears duplicated: 100% identity over 100% of the contig. contig length: 15153
scaffold_27 appears duplicated: 100% identity over 100% of the contig. contig length: 427039
-----------------------------------------------
6 input contigs; 6 larger than 500 bp; 3 duplicated; 3 written to file
#########################################################
SUCCESS: `funannotate clean` test complete.
#########################################################

#########################################################
Running `funannotate mask` unit testing: RepeatModeler --> RepeatMasker
CMD: funannotate mask -i test.fa -o test.masked.fa --cpus 8
#########################################################
-------------------------------------------------------
[10:59 AM]: OS: linux2, 20 cores, ~ 131 GB RAM. Python: 2.7.15
[10:59 AM]: Running funanotate v1.7.2
[10:59 AM]: Soft-masking simple repeats with tantan
[10:59 AM]: Repeat soft-masking finished: 
Masked genome: /crex/proj/uppstore2018213/homap/test-mask_7062/test.masked.fa
num scaffolds: 2
assembly size: 1,216,048 bp
masked repeats: 50,965 bp (4.19%)
-------------------------------------------------------
#########################################################
SUCCESS: `funannotate mask` test complete.
#########################################################

#########################################################
Running `funannotate predict` unit testing
CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 8 --species Awesome testicus
#########################################################
-------------------------------------------------------
[10:59 AM]: OS: linux2, 20 cores, ~ 131 GB RAM. Python: 2.7.15
[10:59 AM]: Running funannotate v1.7.2
Traceback (most recent call last):
  File "/proj/uppstore2018213/PROJ_ENVS/funannotate/bin/funannotate", line 657, in <module>
    main()
  File "/proj/uppstore2018213/PROJ_ENVS/funannotate/bin/funannotate", line 647, in main
    mod.main(arguments)
  File "/proj/uppstore2018213/PROJ_ENVS/funannotate/lib/python2.7/site-packages/funannotate/predict.py", line 426, in main
    for f in os.listdir(os.path.join(LOCALAUGUSTUS, 'species', aug_species)):
OSError: [Errno 2] No such file or directory: 'annotate/predict_misc/ab_initio_parameters/augustus/species/saccharomyces'
#########################################################
Traceback (most recent call last):
  File "/proj/uppstore2018213/PROJ_ENVS/funannotate/bin/funannotate", line 657, in <module>
    main()
  File "/proj/uppstore2018213/PROJ_ENVS/funannotate/bin/funannotate", line 647, in main
    mod.main(arguments)
  File "/proj/uppstore2018213/PROJ_ENVS/funannotate/lib/python2.7/site-packages/funannotate/test.py", line 389, in main
    runPredictTest(args)
  File "/proj/uppstore2018213/PROJ_ENVS/funannotate/lib/python2.7/site-packages/funannotate/test.py", line 152, in runPredictTest
    tmpdir, 'annotate', 'predict_results', 'Awesome_testicus.gff3')) <= 1800
  File "/proj/uppstore2018213/PROJ_ENVS/funannotate/lib/python2.7/site-packages/funannotate/test.py", line 40, in countGFFgenes
    with open(input, 'rU') as f:
IOError: [Errno 2] No such file or directory: 'test-predict_7062/annotate/predict_results/Awesome_testicus.gff3'

OS/Install Information

You are running Perl v 5.024001. Now checking perl modules... Bio::Perl: 1.007002 Carp: 1.40 Clone: 0.39 DBD::SQLite: 1.54 DBD::mysql: 4.043 DBI: 1.634 DB_File: 1.84 Data::Dumper: 2.160 File::Basename: 2.85 File::Which: 1.21 Getopt::Long: 2.48 Hash::Merge: 0.200 JSON: 4.02 LWP::UserAgent: 6.26 Logger::Simple: 2.0 POSIX: 1.65 Parallel::ForkManager: 1.19 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.11 Text::Soundex: 3.05 Thread::Queue: 3.09 Tie::File: 1.02 URI::Escape: 3.31 YAML: 1.26 threads: 2.07 threads::shared: 1.51 All 27 Perl modules installed

Checking Environmental Variables... $FUNANNOTATE_DB=/crex/proj/uppstore2018213/funannotate_db $PASAHOME=/proj/uppstore2018213/PROJ_ENVS/funannotate/opt/pasa-2.4.1 $TRINITY_HOME=/proj/uppstore2018213/PROJ_ENVS/funannotate/opt/trinity-2.8.5 $EVM_HOME=/proj/uppstore2018213/PROJ_ENVS/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/proj/uppstore2018213/PROJ_ENVS/funannotate/config/ $GENEMARK_PATH=/sw/bioinfo/GeneMark/4.38-es/rackham/gmes_petap.pl All 6 environmental variables are set

Checking external dependencies... PASA: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.3 bamtools: bamtools 2.5.1 bedtools: bedtools v2.29.2 blat: BLAT v36 diamond: 0.9.21 emapper.py: 2.0.1 ete3: 3.1.1 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2017-11-15 gmes_petap.pl: 4.38 hisat2: 2.1.0 hmmscan: HMMER 3.3 (Nov 2019) hmmsearch: HMMER 3.3 (Nov 2019) java: 11.0.1-internal kallisto: 0.46.1 mafft: v7.455 (2019/Dec/7) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.17-r941 proteinortho: 6.0.12 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.9 signalp: 4.1 snap: 2006-07-28 stringtie: 2.0 tRNAscan-SE: 2.0.5 (October 2019) tantan: tantan 13 tbl2asn: no way to determine, likely 25.X tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 All 36 external dependencies are installed`

Thank you very much for your help

nextgenusfs commented 4 years ago

Might just be the Augustus version. What is the output of “funannotate species” command? Is saccharomyces in that table?

Homap commented 4 years ago

Thanks a lot for your reply. The output of funannotate species is as follows:

Species                                    Augustus               GeneMark   Snap   GlimmerHMM   CodingQuarry   Date       
  Conidiobolus_coronatus                     augustus pre-trained   None       None   None         None           2020-03-24
  E_coli_K12                                 augustus pre-trained   None       None   None         None           2020-03-24
  Xipophorus_maculatus                       augustus pre-trained   None       None   None         None           2020-03-24
  adorsata                                   augustus pre-trained   None       None   None         None           2020-03-24
  aedes                                      augustus pre-trained   None       None   None         None           2020-03-24
  amphimedon                                 augustus pre-trained   None       None   None         None           2020-03-24
  ancylostoma_ceylanicum                     augustus pre-trained   None       None   None         None           2020-03-24
  anidulans                                  augustus pre-trained   None       None   None         None           2020-03-24
  arabidopsis                                augustus pre-trained   None       None   None         None           2020-03-24
  aspergillus_fumigatus                      augustus pre-trained   None       None   None         None           2020-03-24
  aspergillus_nidulans                       augustus pre-trained   None       None   None         None           2020-03-24
  aspergillus_oryzae                         augustus pre-trained   None       None   None         None           2020-03-24
  aspergillus_terreus                        augustus pre-trained   None       None   None         None           2020-03-24
  b_pseudomallei                             augustus pre-trained   None       None   None         None           2020-03-24
  bombus_impatiens1                          augustus pre-trained   None       None   None         None           2020-03-24
  bombus_terrestris2                         augustus pre-trained   None       None   None         None           2020-03-24
  botrytis_cinerea                           augustus pre-trained   None       None   None         None           2020-03-24
  brugia                                     augustus pre-trained   None       None   None         None           2020-03-24
  c_elegans_trsk                             augustus pre-trained   None       None   None         None           2020-03-24
  cacao                                      augustus pre-trained   None       None   None         None           2020-03-24
  caenorhabditis                             augustus pre-trained   None       None   None         None           2020-03-24
  camponotus_floridanus                      augustus pre-trained   None       None   None         None           2020-03-24
  candida_albicans                           augustus pre-trained   None       None   None         None           2020-03-24
  candida_guilliermondii                     augustus pre-trained   None       None   None         None           2020-03-24
  candida_tropicalis                         augustus pre-trained   None       None   None         None           2020-03-24
  chaetomium_globosum                        augustus pre-trained   None       None   None         None           2020-03-24
  chicken                                    augustus pre-trained   None       None   None         None           2020-03-24
  chiloscyllium                              augustus pre-trained   None       None   None         None           2020-03-24
  chlamy2011                                 augustus pre-trained   None       None   None         None           2020-03-24
  chlamydomonas                              augustus pre-trained   None       None   None         None           2020-03-24
  chlorella                                  augustus pre-trained   None       None   None         None           2020-03-24
  ciona                                      augustus pre-trained   None       None   None         None           2020-03-24
  coccidioides_immitis                       augustus pre-trained   None       None   None         None           2020-03-24
  coprinus                                   augustus pre-trained   None       None   None         None           2020-03-24
  coprinus_cinereus                          augustus pre-trained   None       None   None         None           2020-03-24
  coyote_tobacco                             augustus pre-trained   None       None   None         None           2020-03-24
  cryptococcus                               augustus pre-trained   None       None   None         None           2020-03-24
  cryptococcus_neoformans_gattii             augustus pre-trained   None       None   None         None           2020-03-24
  cryptococcus_neoformans_neoformans_B       augustus pre-trained   None       None   None         None           2020-03-24
  cryptococcus_neoformans_neoformans_JEC21   augustus pre-trained   None       None   None         None           2020-03-24
  culex                                      augustus pre-trained   None       None   None         None           2020-03-24
  debaryomyces_hansenii                      augustus pre-trained   None       None   None         None           2020-03-24
  elephant_shark                             augustus pre-trained   None       None   None         None           2020-03-24
  encephalitozoon_cuniculi_GB                augustus pre-trained   None       None   None         None           2020-03-24
  eremothecium_gossypii                      augustus pre-trained   None       None   None         None           2020-03-24
  fly                                        augustus pre-trained   None       None   None         None           2020-03-24
  fly_exp                                    augustus pre-trained   None       None   None         None           2020-03-24
  fusarium                                   augustus pre-trained   None       None   None         None           2020-03-24
  fusarium_graminearum                       augustus pre-trained   None       None   None         None           2020-03-24
  galdieria                                  augustus pre-trained   None       None   None         None           2020-03-24
  generic                                    augustus pre-trained   None       None   None         None           2020-03-24
  heliconius_melpomene1                      augustus pre-trained   None       None   None         None           2020-03-24
  histoplasma                                augustus pre-trained   None       None   None         None           2020-03-24
  histoplasma_capsulatum                     augustus pre-trained   None       None   None         None           2020-03-24
  honeybee1                                  augustus pre-trained   None       None   None         None           2020-03-24
  human                                      augustus pre-trained   None       None   None         None           2020-03-24
  japaneselamprey                            augustus pre-trained   None       None   None         None           2020-03-24
  kluyveromyces_lactis                       augustus pre-trained   None       None   None         None           2020-03-24
  laccaria_bicolor                           augustus pre-trained   None       None   None         None           2020-03-24
  leishmania_tarentolae                      augustus pre-trained   None       None   None         None           2020-03-24
  lodderomyces_elongisporus                  augustus pre-trained   None       None   None         None           2020-03-24
  magnaporthe_grisea                         augustus pre-trained   None       None   None         None           2020-03-24
  maize                                      augustus pre-trained   None       None   None         None           2020-03-24
  maize5                                     augustus pre-trained   None       None   None         None           2020-03-24
  mnemiopsis_leidyi                          augustus pre-trained   None       None   None         None           2020-03-24
  nasonia                                    augustus pre-trained   None       None   None         None           2020-03-24
  nematostella_vectensis                     augustus pre-trained   None       None   None         None           2020-03-24
  neurospora                                 augustus pre-trained   None       None   None         None           2020-03-24
  neurospora_crassa                          augustus pre-trained   None       None   None         None           2020-03-24
  parasteatoda                               augustus pre-trained   None       None   None         None           2020-03-24
  pchrysosporium                             augustus pre-trained   None       None   None         None           2020-03-24
  pea_aphid                                  augustus pre-trained   None       None   None         None           2020-03-24
  pfalciparum                                augustus pre-trained   None       None   None         None           2020-03-24
  phanerochaete_chrysosporium                augustus pre-trained   None       None   None         None           2020-03-24
  pichia_stipitis                            augustus pre-trained   None       None   None         None           2020-03-24
  pisaster                                   augustus pre-trained   None       None   None         None           2020-03-24
  pneumocystis                               augustus pre-trained   None       None   None         None           2020-03-24
  rhincodon                                  augustus pre-trained   None       None   None         None           2020-03-24
  rhizopus_oryzae                            augustus pre-trained   None       None   None         None           2020-03-24
  rhodnius                                   augustus pre-trained   None       None   None         None           2020-03-24
  rice                                       augustus pre-trained   None       None   None         None           2020-03-24
  s_aureus                                   augustus pre-trained   None       None   None         None           2020-03-24
  s_pneumoniae                               augustus pre-trained   None       None   None         None           2020-03-24
  saccharomyces                              augustus pre-trained   None       None   None         None           2020-03-24
  saccharomyces_cerevisiae_S288C             augustus pre-trained   None       None   None         None           2020-03-24
  saccharomyces_cerevisiae_rm11-1a_1         augustus pre-trained   None       None   None         None           2020-03-24
  schistosoma                                augustus pre-trained   None       None   None         None           2020-03-24
  schistosoma2                               augustus pre-trained   None       None   None         None           2020-03-24
  schizosaccharomyces_pombe                  augustus pre-trained   None       None   None         None           2020-03-24
  scyliorhinus                               augustus pre-trained   None       None   None         None           2020-03-24
  sealamprey                                 augustus pre-trained   None       None   None         None           2020-03-24
  strongylocentrotus_purpuratus              augustus pre-trained   None       None   None         None           2020-03-24
  sulfolobus_solfataricus                    augustus pre-trained   None       None   None         None           2020-03-24
  template_prokaryotic                       augustus pre-trained   None       None   None         None           2020-03-24
  tetrahymena                                augustus pre-trained   None       None   None         None           2020-03-24
  thermoanaerobacter_tengcongensis           augustus pre-trained   None       None   None         None           2020-03-24
  tomato                                     augustus pre-trained   None       None   None         None           2020-03-24
  toxoplasma                                 augustus pre-trained   None       None   None         None           2020-03-24
  tribolium2012                              augustus pre-trained   None       None   None         None           2020-03-24
  trichinella                                augustus pre-trained   None       None   None         None           2020-03-24
  ustilago                                   augustus pre-trained   None       None   None         None           2020-03-24
  ustilago_maydis                            augustus pre-trained   None       None   None         None           2020-03-24
  verticillium_albo_atrum1                   augustus pre-trained   None       None   None         None           2020-03-24
  verticillium_longisporum1                  augustus pre-trained   None       None   None         None           2020-03-24
  volvox                                     augustus pre-trained   None       None   None         None           2020-03-24
  wheat                                      augustus pre-trained   None       None   None         None           2020-03-24
  yarrowia_lipolytica                        augustus pre-trained   None       None   None         None           2020-03-24
  zebrafish                                  augustus pre-trained   None       None   None         None           2020-03-24

Options for this script:
 To print a parameter file to terminal:
   funannotate species -p myparameters.json
 To print the parameters details from a species in the database:
   funannotate species -s aspergillus_fumigatus
 To add a new species to database:
   funannotate species -s new_species_name -a new_species_name.parameters.json
pavlohrab commented 4 years ago

I have the same issue. Have you managed to solve it?