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    Camille Scott
    @camillescott
    And there we go, a dammit gitter room!
    @macmanes at your request :)
    Matt MacManes
    @macmanes
    YAY!!!
    Matt MacManes
    @macmanes
    can I assume that signalP not a part of the package as the license is obtuse?
    Camille Scott
    @camillescott
    yeah, it doesn't meet the accessibility requirement
    needing an academic email and registration and all
    not sure if there's a replacement for it, i ought to do some looking
    Camille Scott
    @camillescott
    Hello @all! A new version of dammit, v 0.2.3, has been released and is available through PyPI. This version fixes the bug with reported HMMER coordinates; if your analyses rely on these coordinates, it is strongly recommended that you upgrade. More info is available on the releases page on github: https://github.com/camillescott/dammit/releases
    Camille Scott
    @camillescott
    hi all @channel, for those interested, complete uniref90 support is back and working on the master branch with the --full flag
    it should be in a new release within a day or so
    Matt MacManes
    @macmanes
    ok, @camillescott, is the official name dammit! or dammit
    (important question) :)
    Camille Scott
    @camillescott
    HI @/all , version 0.2.4 has been released!
    @macmanes, although i'd prefer dammit!, i think i might just go with dammit, because it's less awkward to use in sentences XD
    Matt MacManes
    @macmanes
    gotcha!
    Jordi
    @jordur

    Hi all! I am trying to install dammit! to annotate my data and I get the following error:

    ERROR:  Loading command: install (LoadError)
    cannot load such file -- openssl
    ERROR:  While executing gem ... (NoMethodError)
    undefined method `invoke_with_build_args' for nil:NilClass

    I have been able to install ruby ruby 2.0.0p481 (2014-05-08 revision 45883) [x86_64-linux] and I tried sudo gem install crb-blast
    What I am doing wrong? Thank you

    Jordi
    @jordur
    That's it! A couple of libreries I haven't had installled: libssl1.0.0 and libssl-dev
    Lisa K. Johnson
    @ljcohen
    dammit! running on UCD farm cluster!
    Matt MacManes
    @macmanes
    yay!!!
    how many compute nodes is that?
    obviously hmmer is still gonna be a major time-suck
    Lisa K. Johnson
    @ljcohen
    blob
    This message was deleted
    it's a small cluster for ag and env sci, i think ~50 nodes
    i should know more about this
    Jordi
    @jordur
    hi! I ran dammit and I got the following error:
    Some tasks failed![dammit.annotate:ERROR]
    TaskError - taskid:remap_hmmer:longest_orfs.pep.pfam.tbl[dammit.annotate:ERROR]
    PythonAction Error
    Traceback (most recent call last):
      File "/home/bec2-jcalvete/anaconda2/lib/python2.7/site-packages/doit/action.py", line 383, in execute
        returned_value = self.py_callable(*self.args, **kwargs)
      File "/home/bec2-jcalvete/anaconda2/lib/python2.7/site-packages/dammit/tasks.py", line 472, in cmd
        assert(all(hmmer_df.env_coord_to <= merged_df.end))
    AssertionError
    [dammit.annotate:ERROR]
    Some tasks failed![dammit.annotate:ERROR]
    TaskFailed - taskid:TransDecoder.Predict:transfuse_18_cons.fa[dammit.annotate:ERROR]
    Command failed: '/media/bec2-jcalvete/Disc_Dur/Feina_Jordi/programes/TransDecoder-2.0.1/TransDecoder.Predict -t transfuse_18_cons.fa --retain_pfam_hits transfuse_18_cons.fa.transdecoder_dir/longest_orfs.pep.pfam.tbl             --retain_long_orfs 600' returned 2
    [dammit.annotate:ERROR]
    Some tasks failed![dammit.annotate:ERROR]
    UnmetDependency - taskid:hmmscan-gff3:transfuse_18_cons.fa.pfam.csv.gff3[dammit.annotate:ERROR]
    remap_hmmer:longest_orfs.pep.pfam.tbl
    [dammit.annotate:ERROR]
    Some tasks failed![dammit.annotate:ERROR]
    UnmetDependency - taskid:gff3-merge:transfuse_18_cons.fa.dammit.gff3[dammit.annotate:ERROR]
    hmmscan-gff3:transfuse_18_cons.fa.pfam.csv.gff3 TransDecoder.Predict:transfuse_18_cons.fa
    [dammit.annotate:ERROR]
    Some tasks failed![dammit.annotate:ERROR]
    UnmetDependency - taskid:fasta-annotate:transfuse_18_cons.fa.dammit.fasta[dammit.annotate:ERROR]
    gff3-merge:transfuse_18_cons.fa.dammit.gff3
    [dammit.annotate:ERROR]
    which do you think could be the source of the error?
    Thanks
    Camille Scott
    @camillescott
    hi @jordur! this bug was fixed in the most recent release of dammit; you can get it with:
    pip install dammit -U --no-deps
    Jordi
    @jordur
    ok, thank you @camillescott . I will install the newest version. Sorry for the inconvenience.
    Camille Scott
    @camillescott
    no prob :) i really need to create a mailing list
    ulrichkudahl
    @ulrichkudahl
    Hi Cammile. Great tool you have created, however I struggle a bit getting it to work on on OS X. I keep getting the following error and don't quite know how to attack the problem
    '''
    Some tasks failed![dammit.annotate:ERROR]
    TaskFailed - taskid:hmmscan:longest_orfs.pep.x.Pfam-A.hmm[dammit.annotate:ERROR]
    Command failed: 'S=stat -c "%s" test2.fasta.transdecoder_dir/longest_orfs.pep; B=expr $S / 1; cat test2.fasta.transdecoder_dir/longest_orfs.pep | /usr/local/bin/parallel --block $B --pipe --recstart ">" --gnu -j 1 /usr/local/bin/hmmscan --cpu 1 --domtblout /dev/stdout -E 1e-05 -o test2.fasta.transdecoder_dir/longest_orfs.pep.pfam.tbl.out /Users/Ulrich/.dammit/databases/Pfam-A.hmm /dev/stdin > test2.fasta.transdecoder_dir/longest_orfs.pep.pfam.tbl' returned 20
    '''
    Camille Scott
    @camillescott
    hi @ulrichkudahl! thanks :)
    i'm gonna guess that its a problem with gnu parallel
    can you try running which parallel?
    ulrichkudahl
    @ulrichkudahl
    "/usr/local/bin/parallel"
    Camille Scott
    @camillescott
    gotcha
    in that case
    do tail -n 500 ~/.dammit/log/dammit-all.log and post the result here :)
    ulrichkudahl
    @ulrichkudahl

    04-22 22:52:30 dammit.annotate:write:85 [INFO]

    [x] transcriptome_stats:test2.fasta

    04-22 22:52:30 dammit.annotate:write:85 [INFO]

    [x] busco:test2.fasta-metazoa

    04-22 22:52:30 dammit.annotate:write:85 [INFO]

    [x] TransDecoder.LongOrfs:test2.fasta

    04-22 22:52:30 dammit.annotate:write:85 [INFO]

    [ ] hmmscan:longest_orfs.pep.x.Pfam-A.hmm

    04-22 22:52:30 dammit.annotate:write:85 [ERROR]

    Some tasks failed!

    04-22 22:52:30 dammit.annotate:write:85 [ERROR]

    TaskFailed - taskid:hmmscan:longest_orfs.pep.x.Pfam-A.hmm

    04-22 22:52:30 dammit.annotate:write:85 [ERROR]
    Command failed: 'S=stat -c "%s" test2.fasta.transdecoder_dir/longest_orfs.pep; B=expr $S / 1; cat test2.fasta.transdecoder_dir/longest_orfs.pep | /usr/local/bin/parallel --block $B --pipe --recstart ">" --gnu -j 1 /usr/local/bin/hmmscan --cpu 1 --domtblout /dev/stdout -E 1e-05 -o test2.fasta.transdecoder_dir/longest_orfs.pep.pfam.tbl.out /Users/Ulrich/.dammit/databases/Pfam-A.hmm /dev/stdin > test2.fasta.transdecoder_dir/longest_orfs.pep.pfam.tbl' returned 20


    04-22 22:52:30 dammit.annotate:write:85 [DEBUG]


    04-22 22:52:30 dammit.annotate:write:85 [DEBUG]
    stat: illegal option -- c
    usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file ...]
    expr: syntax error


    Camille Scott
    @camillescott
    ahhh
    looks like this is one of those "OSX install *nix utilities with the same name/purpose and slightly different options" problems
    ulrichkudahl
    @ulrichkudahl
    Yes, the stat command doesn't respond to the -c option
    Camille Scott
    @camillescott
    alrighty, here's what i'll do
    i'll push a fix to github in a bit
    and you can pip install using the dev instructions
    ulrichkudahl
    @ulrichkudahl