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gjospin / PhyloSift

Phylogenetic and taxonomic analysis for genomes and metagenomes
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installation issue #444

Closed kgwin1 closed 10 years ago

kgwin1 commented 10 years ago

I get the following message after installing: Can't locate App/Cmd/Setup.pm in @INC (@INC contains: /home/localuser/Desktop/PhyloSift/bin/../lib /home/localuser/Desktop/PhyloSift/version-0.9902/lib/ /home/localuser/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/x86_64-linux /home/localuser/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0 /home/localuser/perl5/perlbrew/perls/perl-5.16.0/lib/5.16.0/x86_64-linux /home/localuser/perl5/perlbrew/perls/perl-5.16.0/lib/5.16.0 .) at /home/localuser/Desktop/PhyloSift/bin/../lib/Phylosift.pm line 2. BEGIN failed--compilation aborted at /home/localuser/Desktop/PhyloSift/bin/../lib/Phylosift.pm line 2. Compilation failed in require at /home/localuser/Desktop/PhyloSift/bin/phylosift line 6. BEGIN failed--compilation aborted at /home/localuser/Desktop/PhyloSift/bin/phylosift line 6. Any suggestions? Thanks!

koadman commented 10 years ago

Hi kgwin1, what did you do to "install" phylosift? You should be able to run it without any kind of installation, just unpack the archive and run. Is that what you've done?

kgwin1 commented 10 years ago

I ran git clone git://github.com/gjospin/PhyloSift.git

kgwin1 commented 10 years ago

Nevermind, I have since deleted that and reinstalled via website and unzipped! Now it works.

gjospin commented 10 years ago

Excellent, I was about to suggest that. Thanks for letting us know.

On Thu, Dec 5, 2013 at 1:56 PM, Kelley Nunez notifications@github.comwrote:

Nevermind, I have since deleted that and reinstalled via website and unzipped! Now it works.

— Reply to this email directly or view it on GitHubhttps://github.com/gjospin/PhyloSift/issues/444#issuecomment-29942476 .

kgwin1 commented 10 years ago

Just another quick question: running the whole workflow with the all command gives me this error: rm: cannot remove `/home/localuser/Desktop/phylosift_v1.0.0_02/PS_temp/simulated_BEI200.01percent.fasta/blastDir/.aa.1_': No such file or directory

Am I missing something?

gjospin commented 10 years ago

The files resulting from the search step get deleted automatically (unless --debug is used --keep_search I think). It could be that you didn't get any hits and there were no files to remove. It could also be that you have uncovered a bug that needs fixing.

Are you getting results such as a krona plot or anything in the alignDir or treeDir directories? If you are seeing results files, I wouldn't worry too much about the message you reported as it's just trying to delete something that is not there. It would not be hurting the end results.

I am assuming you have downloaded the marker database and indexed it prior to running the workflow. No index would mean no search hits but there would have been a nasty error if that happened.

On Thu, Dec 5, 2013 at 2:00 PM, Kelley Nunez notifications@github.comwrote:

Just another quick question: running the whole workflow with the all command gives me this error: rm: cannot remove `/home/localuser/Desktop/phylosift_v1.0.0_02/PS_temp/simulated_BEI200.01percent.fasta/blastDir/ .aa.1_': No such file or directory

Am I missing something?

— Reply to this email directly or view it on GitHubhttps://github.com/gjospin/PhyloSift/issues/444#issuecomment-29942854 .

kgwin1 commented 10 years ago

No, I am not seeing anything in treeDir or alignDir. No I have not downloaded the marker database or indexed it. Was the 16S database not included?

gjospin commented 10 years ago

It should automatically download the marker DB when you start Phylosift. I would recommend running the following command just to make sure.

./phylosift index

On Thu, Dec 5, 2013 at 2:43 PM, Kelley Nunez notifications@github.comwrote:

No, I am not seeing anything in treeDir or alignDir. No I have not downloaded the marker database or indexed it. Was the 16S database not included?

— Reply to this email directly or view it on GitHubhttps://github.com/gjospin/PhyloSift/issues/444#issuecomment-29946416 .

kgwin1 commented 10 years ago

Okay. I tried that and got the same error message. I'm inputting a fasta file and the program is straight forward. Am I missing something else? My command: ./phylosift all $HOME/simulated_data.fasta'

gjospin commented 10 years ago

Check $HOME/share/phylosift to make sure you have the database downloaded. You should have a markers directory (with about 850 markers) and a ncbi directory with a few files related to taxonomy.

What system are you running PS on? Could you provide an output dump when running your command using the --debug flag. This would help figure out what is going wrong.

On Thu, Dec 5, 2013 at 3:02 PM, Kelley Nunez notifications@github.comwrote:

Okay. I tried that and got the same error message. I'm inputting a fasta file and the program is straight forward. Am I missing something else? My command: ./phylosift all $HOME/simulated_data.fasta'

— Reply to this email directly or view it on GitHubhttps://github.com/gjospin/PhyloSift/issues/444#issuecomment-29947924 .

kgwin1 commented 10 years ago

Here is the output. Thanks again for all your help!

FORCE: 1 Continue : force : 1 PhyloSift -- Phylogenetic analysis of genomes and metagenomes (c) 2011, 2012 Aaron Darling and Guillaume Jospin

CITATION: PhyloSift. A. E. Darling, G. Jospin, E. Lowe, F. A. Matsen, H. M. Bik, J. A. Eisen. Submitted to PeerJ

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.

Before START 2013-12-06 08:27:24 All systems are good to go, continuing the screening MODE : all Using updated markers Using a marker list file /home/localuser/share/phylosift/markers/marker_list.txt Before runBlast 2013-12-06 08:27:24 USING 0 Input type is dna, fasta Making fifos Launching search process 1 Running /home/localuser/Desktop/phylosift_v1.0.0_02/bin/lastal -F15 -e75 -f0 /home/localuser/share/phylosift/markers/replast "/home/localuser/Desktop/phylosift_v1.0.0_02/PS_temp/simulated_BEI20_0.01percent.fasta/blastDir/last_0.pipe" |Opening /home/localuser/Desktop/phylosift_v1.0.0_02/PS_temp/simulated_BEI20_0.01percent.fasta/blastDir/reads.fasta.1 Octopus is handing out sequences Octopus handed out 15200 sequences Writing candidates from process 1 ReadsFile: /home/localuser/Desktop/Qiime_supermike/simulated_data_100bp/simulated_BEI20_0.01percent.fasta .lastal Got 0 markers with hits .lastal Got 0 nucleotide markers with hits After runBlast 2013-12-06 08:27:24 Before runAlign 2013-12-06 08:27:24 after marker prep AFTER ALIGN and MASK Using a marker list file /home/localuser/share/phylosift/markers/marker_list.txt Using a marker list file /home/localuser/share/phylosift/markers/marker_list.txt AFTER concatenateALI After runAlign 2013-12-06 08:27:24 Before runPplacer 2013-12-06 08:27:24 After runPplacer 2013-12-06 08:27:24 Before runSummarize 2013-12-06 08:27:24

**STARTING SUMMARY

Writing sequences Total classifiable probability mass is 0 Before runKrona 2013-12-06 08:27:24 Generating krona After runKrona 2013-12-06 08:27:24 Debug lvl : 1 After runBlast 2013-12-06 08:27:24 MODE :: all After START 2013-12-06 08:27:24

kgwin1 commented 10 years ago

I'm using a simulated dataset composed of 100b randomly chopped 16S sequences from 20 bacterial species to test the program and see what the outputs are.

kgwin1 commented 10 years ago

This may be the issue, my marker_list.txt is blank. I'm not sure how that happened

koadman commented 10 years ago

Hi Kelley, that is definitely a problem. I'm not sure how it happened but can suggest a course of action to resolve it. First delete the marker_list.txt and then re-run phylosift index --debug. If that doesn't solve the problem you can delete the entire marker directory, which should trigger a re-download and index next time you run PhyloSift. Hope that helps.

On Fri, 2013-12-06 at 07:01 -0800, Kelley Nunez wrote:

This may be the issue, my marker_list.txt is blank. I'm not sure how that happened

— Reply to this email directly or view it on GitHub.