Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
    Jordi
    @jordur
    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
    if you can find your site-packages directory, you can edit the file. something like /path/to/python/lib/python2.7/site-packages/dammit
    there's a file in there called .config.json
    one group is called "last", and has an entry for "lastdb"
    you can add extra arguments to its params entry, and they will be used in the run
    there is a bunch of info about tuning here: http://last.cbrc.jp/doc/last-tuning.html
    the only extra param included by default is -w3
    this reduces memory usage
    you can up that to -w5 or more
    there are tradeoffs, explained in the last docs i linked
    hope that helps @ulrichkudahl :)
    future version will probably allow for more tuning (ie passing in your own config file)