This one may be a little out of my wheelhouse, but did you verify that the
reference it's trying to use is available?  Does this same job work if you
try it on galaxy main (if that's an option)?

reference=/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa


On Wed, May 1, 2013 at 8:41 AM, Iry Witham <iry.wit...@jax.org> wrote:

>  Hi Dannon,
>
>  I was able to get cmake installed and then reinstalled Freebayes just
> fine.  However, I now am getting the following error: *unable to find
> FASTA index entry for '1'*. The resulting files is:
>
>    Chrom Pos ID Ref Alt Qual Filter Info Format data  ##fileformat=VCFv4.1
> ##fileDate=20130501  ##source=freeBayes version 0.9.6
> ##reference=/mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa
> ##phasing=none  ##commandline="freebayes --bam localbam_0.bam
> --fasta-reference /mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa
> --vcf /mnt/galaxyData/files/000/dataset_101.dat"  
> ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number
> of samples with data">  ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total
> read depth at the locus">  
> ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total
> number of alternate alleles in called genotypes">  
> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total
> number of alleles in called genotypes">  
> ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated
> allele frequency in the range (0,1]">  
> ##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference
> allele observations">  
> ##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate
> allele observations">  ##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand
> balance probability for the reference allele: Phred-scaled upper-bounds
> estimate of the probability of observing the deviation between SRF and SRR
> given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">  
> ##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand
> balance probability for the alternate allele: Phred-scaled upper-bounds
> estimate of the probability of observing the deviation between SAF and SAR
> given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">  
> ##INFO=<ID=AB,Number=A,Type=Float,Description="Allele
> balance at heterozygous sites: a number between 0 and 1 representing the
> ratio of reads showing the reference allele to all reads, considering only
> reads from individuals called as heterozygous">  
> ##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele
> balance probability at heterozygous sites: Phred-scaled upper-bounds
> estimate of the probability of observing the deviation between ABR and ABA
> given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">  
> ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run
> length: the number of consecutive repeats of the alternate allele in the
> reference genome">  ##INFO=<ID=RPP,Number=A,Type=Float,Description="Read
> Placement Probability: Phred-scaled upper-bounds estimate of the
> probability of observing the deviation between RPL and RPR given E(RPL/RPR)
> ~ 0.5, derived using Hoeffding's inequality">  
> ##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read
> Placement Probability for reference observations: Phred-scaled upper-bounds
> estimate of the probability of observing the deviation between RPL and RPR
> given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">  
> ##INFO=<ID=EPP,Number=A,Type=Float,Description="End
> Placement Probability: Phred-scaled upper-bounds estimate of the
> probability of observing the deviation between EL and ER given E(EL/ER) ~
> 0.5, derived using Hoeffding's inequality">  
> ##INFO=<ID=EPPR,Number=1,Type=Float,Description="End
> Placement Probability for reference observations: Phred-scaled upper-bounds
> estimate of the probability of observing the deviation between EL and ER
> given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">  
> ##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate
> allele depth ratio. Ratio between depth in samples with each called
> alternate allele and those without.">  
> ##INFO=<ID=XRM,Number=1,Type=Float,Description="Reference
> allele read mismatch rate: The rate of SNPs + MNPs + INDELs in reads
> supporting the reference allele.">  
> ##INFO=<ID=XRS,Number=1,Type=Float,Description="Reference
> allele read SNP rate: The rate of per-base mismatches (SNPs + MNPs) in
> reads supporting the reference allele.">  
> ##INFO=<ID=XRI,Number=1,Type=Float,Description="Reference
> allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the
> reference allele.">  ##INFO=<ID=XAM,Number=A,Type=Float,Description="Alternate
> allele read mismatch rate: The rate of SNPs + MNPs + INDELs in reads
> supporting the alternate allele, excluding the called variant.">  
> ##INFO=<ID=XAS,Number=A,Type=Float,Description="Alternate
> allele read SNP rate: The rate of per-base mismatches (SNPs + MNPs) in
> reads supporting the alternate allele, excluding the called variant.">  
> ##INFO=<ID=XAI,Number=A,Type=Float,Description="Alternate
> allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the
> alternate allele, excluding the called variant.">  
> ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The
> log odds ratio of the best genotype combination to the second-best.">  
> ##INFO=<ID=BVAR,Number=0,Type=Flag,Description="The
> best genotype combination in the posterior is variant (non homozygous).">  
> ##INFO=<ID=CpG,Number=0,Type=Flag,Description="CpG
> site (either CpG, TpG or CpA)">  
> ##INFO=<ID=TYPE,Number=A,Type=String,Description="The
> type of allele, either snp, mnp, ins, del, or complex.">  
> ##INFO=<ID=CIGAR,Number=A,Type=String,Description="The
> extended CIGAR representation of each alternate allele, with the exception
> that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do
> not have the first matched base (which is provided by default, per the
> spec) referred to by the CIGAR.">  
> ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number
> of unique non-reference alleles in called genotypes at this position.">  
> ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean
> number of unique non-reference allele observations per sample with the
> corresponding alternate alleles.">  
> ##INFO=<ID=HWE,Number=1,Type=Float,Description="Phred-scaled
> discrete HWE prior probability of the genotyping across all samples.">  
> ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele
> length">  ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping
> quality of observed alternate alleles">  
> ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean
> mapping quality of observed reference alleles">  
> ##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion
> of observed alternate alleles which are supported by properly paired read
> fragments">  ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion
> of observed reference alleles which are supported by properly paired read
> fragments">  ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">  
> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype
> Quality, the Phred-scaled marginal (or unconditional) probability of the
> called genotype">  ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype
> Likelihood, log10-scaled likelihoods of the data given the called genotype
> for each possible genotype generated from the reference and alternate
> alleles given the sample ploidy">  
> ##FORMAT=<ID=GLE,Number=1,Type=String,Description="Genotype
> Likelihood Explicit, same as GL, but with tags to indicate the specific
> genotype. For instance,
> 0^-75.22|1^-223.42|0/0^-323.03|1/0^-99.29|1/1^-802.53 represents both
> haploid and diploid genotype likilehoods in a biallelic context">  
> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read
> Depth">  ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference
> allele observation count">  
> ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum
> of quality of the reference observations">  
> ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate
> allele observation count">  
> ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum
> of quality of the alternate observations">  #CHROM POS ID REF ALT QUAL
> FILTER INFO FORMAT unknown
>
>  Iry
>
>   From: Dannon Baker <dannon.ba...@gmail.com>
> Date: Tuesday, April 30, 2013 1:06 PM
> To: Iry Witham <iry.wit...@jax.org>
> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
> Subject: Re: [galaxy-dev] Installing FreeBayes via Toolshed: Tool
> dependency installation error
>
>   Looks like you're missing cmake, a dependency for building FreeBayes.
>  If you're able to install that for your system (available in most package
> managers) you should be good to go.
>
>  -Dannon
>
>
> On Tue, Apr 30, 2013 at 1:03 PM, Iry Witham <iry.wit...@jax.org> wrote:
>
>>  Hi All,
>>
>>  I am trying to get Freebayes installed on a cloud man instance from the
>> galaxy toolshed.  I have successfully installed the Samtools 0.1.18
>> package, but the freebayes package errors.
>>
>>  The Error is:
>>
>>  Tool shed repository: freebayes
>> Tool shed repository changeset revision: 28e422c589ac
>> Tool dependency status: Error
>> Tool dependency installation error: /bin/sh: cmake: not found
>> make[1]: *** [../bamtools/lib/libbamtools.a] Error 127
>> make: *** [all] Error 2
>> Tool dependency installation directory:
>> /mnt/galaxyTools/tools/freebayes/0.9.6_9608597d12e127c847ae03aa03440ab63992fedf/devteam/freebayes/28e422c589ac
>>
>>  I get the following message after the error occurs:
>>
>>  This tool dependency is not installed correctly (see the *Tool
>> dependency installation error* below). Choose *Uninstall this tool
>> dependency* from the *Repository Actions* menu, correct problems if
>> necessary, and try installing the dependency again.
>>
>>  I have followed this procedure and still have the same error.  I have
>> looked at the Installation.log file and this is what I found:
>>
>>  #############################################
>> git clone --recursive git://github.com/ekg/freebayes.git
>> STDOUT
>> Initialized empty Git repository in
>> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/.git/
>> Submodule 'bamtools' (git://github.com/pezmaster31/bamtools.git)
>> registered for path 'bamtools'
>> Submodule 'intervaltree' (git://github.com/ekg/intervaltree.git)
>> registered for path 'intervaltree'
>> Submodule 'vcflib' (git://github.com/ekg/vcflib.git) registered for path
>> 'vcflib'
>> Initialized empty Git repository in
>> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/bamtools/.git/
>> Submodule path 'bamtools': checked out
>> '3fe66b92028b60629826d827ee9058405fa7e4be'
>> Initialized empty Git repository in
>> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/intervaltree/.git/
>> Submodule path 'intervaltree': checked out
>> 'd151b487804861dc9f932e9f1fe4f8c499673cec'
>> Initialized empty Git repository in
>> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/.git/
>> Submodule path 'vcflib': checked out
>> '480d96e16a552d36369dc9cb2b39ceedb260944a'
>> Submodule 'fastahack' (git://github.com/ekg/fastahack.git) registered
>> for path 'fastahack'
>> Submodule 'fsom' (git://github.com/ekg/fsom.git) registered for path
>> 'fsom'
>> Submodule 'intervaltree' (git://github.com/ekg/intervaltree.git)
>> registered for path 'intervaltree'
>> Submodule 'multichoose' (git://github.com/ekg/multichoose.git)
>> registered for path 'multichoose'
>> Submodule 'smithwaterman' (git://github.com/ekg/smithwaterman.git)
>> registered for path 'smithwaterman'
>> Submodule 'tabixpp' (git://github.com/ekg/tabixpp.git) registered for
>> path 'tabixpp'
>> Initialized empty Git repository in
>> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/fastahack/.git/
>> Submodule path 'fastahack': checked out
>> '6acaf9875f2dbcdf86c9c690a8d188000e90d388'
>> Initialized empty Git repository in
>> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/fsom/.git/
>> Submodule path 'fsom': checked out
>> '1b888f32c4bd571d1a0bea88d39cd7d7f23ea4b8'
>> Initialized empty Git repository in
>> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/intervaltree/.git/
>> Submodule path 'intervaltree': checked out
>> '1290744283cef8076bb8a2968d4899b7228435f4'
>> Initialized empty Git repository in
>> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/multichoose/.git/
>> Submodule path 'multichoose': checked out
>> '73d35daa18bf35729b9ba758041a9247a72484a5'
>> Initialized empty Git repository in
>> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/smithwaterman/.git/
>> Submodule path 'smithwaterman': checked out
>> 'd9724f156c07cf16d00d251bebc20c6383eb6bde'
>> Initialized empty Git repository in
>> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/tabixpp/.git/
>> Submodule path 'tabixpp': checked out
>> 'fbdde774adfc79ca75a65b4321b89b67cd81b921'
>> #############################################
>>
>>  #############################################
>> git clone --recursive git://github.com/ekg/freebayes.git
>> STDERR
>>
>>  #############################################
>>
>>  #############################################
>> git checkout 9608597d12e127c847ae03aa03440ab63992fedf
>> STDOUT
>> M bamtools
>> M vcflib
>> #############################################
>>
>>  #############################################
>> git checkout 9608597d12e127c847ae03aa03440ab63992fedf
>> STDERR
>> Note: checking out '9608597d12e127c847ae03aa03440ab63992fedf'.
>>
>>  You are in 'detached HEAD' state. You can look around, make experimental
>> changes and commit them, and you can discard any commits you make in this
>> state without impacting any branches by performing another checkout.
>>
>>  If you want to create a new branch to retain commits you create, you may
>> do so (now or later) by using -b with the checkout command again. Example:
>>
>>    git checkout -b new_branch_name
>>
>>  HEAD is now at 9608597... example pipeline script
>> #############################################
>>
>>  #############################################
>> git submodule update --recursive
>> STDOUT
>> Submodule path 'bamtools': checked out
>> '8a5d6508d8fc52b25c9129037e44cc448bafebc7'
>> Submodule path 'vcflib': checked out
>> '3f0d5e19596252b858a7f6eff1578e4295f549c8'
>> Submodule path 'fastahack': checked out
>> 'd1bcd7a2d52ee0e2823884c8ede22ce228d3c060'
>> Submodule path 'smithwaterman': checked out
>> '2882633a3b89f820d692a9b3316f4891dc3a1ff8'
>> #############################################
>>
>>  #############################################
>> git submodule update --recursive
>> STDERR
>> warning: unable to rmdir fsom: Directory not empty
>> #############################################
>>
>>  #############################################
>> make
>> STDOUT
>> cd src && make
>> make[1]: Entering directory `/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/src'
>> cd ../bamtools && mkdir -p build && cd build && cmake .. && make
>> make[1]: Leaving directory `/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/src'
>> #############################################
>>
>>  #############################################
>> make
>> STDERR
>> /bin/sh: cmake: not found
>> make[1]: *** [../bamtools/lib/libbamtools.a] Error 127
>> make: *** [all] Error 2
>> #############################################
>>
>>  Any ideas on how to resolve this?
>>
>>  Thanks,
>>
>>  Iry Witham
>>
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