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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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PhyloSift uses path executables rather than built-in version #54

Closed skoren closed 12 years ago

skoren commented 12 years ago

PhyloSift will use a program from the user's path rather than the built-in version in metAMOS/phylosift. This can cause errors if an incorrect version is installed. Example failure:

PhyloSift -- Phylogenetic analysis of genomes and metagenomes (c) 2011, 2012 Aaron Darling and Guillaume Jospin

CITATION: PhyloSift. A. Darling, H. Bik, G. Jospin, J. A. Eisen. Manuscript in preparation

PhyloSift incorporates several other software packages, please consider also citing the following papers:

    pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree.
    Frederick A Matsen, Robin B Kodner, and E Virginia Armbrust
    BMC Bioinformatics 2010, 11:538

    Adaptive seeds tame genomic sequence comparison.
    SM Kielbasa, R Wan, K Sato, P Horton, MC Frith
    Genome Research 2011.

    Infernal 1.0: Inference of RNA alignments
    E. P. Nawrocki, D. L. Kolbe, and S. R. Eddy
    Bioinformatics 25:1335-1337 (2009)

     Bowtie: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
     Langmead B, Trapnell C, Pop M, Salzberg SL. Genome Biol 10:R25.

     HMMER 3.0 (March 2010); http://hmmer.org/
     Copyright (C) 2010 Howard Hughes Medical Institute.
     Freely distributed under the GNU General Public License (GPLv3).

     Phylogenetic Diversity within Seconds.
    Bui Quang Minh, Steffen Klaere and Arndt von Haeseler
    Syst Biol (2006) 55 (5): 769-773.

Running /nfs/bio/sw/bin/pplacer --groups 10 --verbosity 0 -j 8 -c phylosift/markers/concat.updated UMP_reads/DNIU-N32-DN007-lib1/metAMOS_test/Annotate/out/PS_temp/proba.asm.contig/alignDir/concat.trim.fasta Running /nfs/bio/sw/bin/pplacer --verbosity 0 -j 8 -c phylosift/markers/18s_reps.updatedUMP_reads/DNIU-N32-DN007-lib1/metAMOS_test/Annotate/out/PS_temp/proba.asm.contig/alignDir/18s_reps.trim.fasta Running /nfs/bio/sw/bin/pplacer --verbosity 0 -j 8 -c phylosift/markers/16s_reps_bac.updated UMP_reads/DNIU-N32-DN007-lib1/metAMOS_test/Annotate/out/PS_temp/proba.asm.contig/alignDir/16s_reps_bac.trim.fasta Useless use of private variable in void context at metaAMOS/treangen-metAMOS-37e78da/phylosift/bin/../lib/Phylosift/pplacer.pm line 87. Warning : a different version of pplacer was found. PhyloSift was tested with pplacer v1.1.alpha10 at metaAMOS/treangen-metAMOS-37e78da/phylosift/bin/../lib/Phylosift/Phylosift.pm line 274 /nfs/bio/sw/bin/pplacer: unknown option `--groups'. pplacer [options] [alignment] -c Specify the path to the reference package. -t Specify the reference tree filename. -r Specify the reference alignment filename. -s Supply a phyml stats.txt or a RAxML info file giving the model parameters. -d Specify the directory containing the reference information. -p Calculate posterior probabilities. -m Substitution model. Protein: are LG, WAG, or JTT. Nucleotides: GTR. --model-freqs Use model frequencies instead of reference alignment frequencies. --gamma-cats Number of categories for discrete gamma model. --gamma-alpha Specify the shape parameter for a discrete gamma model. --ml-tolerance 1st stage branch len optimization tolerance (2nd stage to 1e-5). Default: 0.01. --pp-rel-err Relative error for the posterior probability calculation. Default is 0.01. --unif-prior Use a uniform prior rather than exponential. --start-pend Starting pendant branch length. Default is 0.1. --max-pend Set the maximum ML pendant branch length. Default is 2. --max-strikes Maximum number of strikes for baseball. 0 -> no ball playing. Default is 6. --strike-box Set the size of the strike box in log likelihood units. Default is 3. --max-pitches Set the maximum number of pitches for baseball. Default is 40. --fantasy Desired likelihood cutoff for fantasy baseball mode. 0 -> no fantasy. --fantasy-frac Fraction of fragments to use when running fantasy baseball. Default is 0.1. --write-masked Write alignment masked to the region without gaps in the query. --verbosity Set verbosity level. 0 is silent, and 2 is quite a lot. Default is 1. --out-dir Specify the directory to write place files to. --pretend Only check out the files then report. Do not run the analysis. --diagnostic Write file describing the 'diagnostic' mutations for various clades. --check-like Write out the likelihood of the reference tree, calculated two ways. -j The number of child processes to spawn when doing placements. Default is 2. --version Write out the version number and exit. -help Display this list of options --help Display this list of options Fatal error: exception Failure("please specify a reference tree with -t or -c") Fatal error: exception Failure("please specify a reference tree with -t or -c")

koadman commented 12 years ago

This issue was resolved a couple weeks ago in phylosift master/devel branches, commit 80033c8b0b7b56c8a2189a74f55840a3dec4eaf9

Updating the phylosift bundled with metAMOS should resolve this.

skoren commented 12 years ago

Updated to latest phylosift as of today.