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    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
    right?
    Camille Scott
    @camillescott
    yup!
    i'll let you know when i've got a fix
    sorry for this!
    ulrichkudahl
    @ulrichkudahl
    Don't apologise :) I am just amazed that you respond to my query
    Camille Scott
    @camillescott
    haha
    i try to keep an eye on everything, but some problems are easier to diagnose than others ;)
    ulrichkudahl
    @ulrichkudahl
    Hi Camille. Since we spoke last I rented a virtual unix machine and setup dammit there and have successfully run dammit on a set of differentially expressed genes from an RNA-seq study. As an overwhelming about of results files are produced, I am a bit unsure how to approach the analysis side of things. How and with which output files would you recommend starting?
    Matt MacManes
    @macmanes
    Fwiw I basically only use the final fasta and gff3 files which are basically a sum of all the annotation information.
    ulrichkudahl
    @ulrichkudahl
    Thanks again for the quick reply. I suppose I am still a bit unsure about how to really use the GFF3 files, but I will give it a go
    On another note, I tried do to a full install of the databases, but I keep getting an out of memory error. How much memory do you recon I would need do to a full database installation?
    Matt MacManes
    @macmanes
    Memory or hard drive space?
    ulrichkudahl
    @ulrichkudahl
    Memory, but I am also curious to know how much space is required
    *hard drive space is required
    Matt MacManes
    @macmanes
    about use of GFF3. I also use in IGV for viz purposes. Honestly I’ve neved kept track of RAM usage for making te databases. My dammit database folder is 59G
    Camille Scott
    @camillescott
    the databases can be quite memory intensive to generate; expect ~16gb for the orthodb one
    not sure what is necessary for uniref90, though i can try to find out for you
    Camille Scott
    @camillescott
    currently dammit doesn't have an option to custom tune parameters
    however, if you're willing to get a little dirty, you can tune them yourself