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gjospin / PhyloSift

Phylogenetic and taxonomic analysis for genomes and metagenomes
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rm: cannot remove blastDir/*.aa.1* #466

Open xapple opened 9 years ago

xapple commented 9 years ago

Hi !

I just downloaded PhyloSift for a test run to see if the results it generates are interesting for our research or not. But it seems to just output a strange error and then stop.

I installed it and ran it on a simple fasta file containing one sequence like this:

# Install #
cd ~/test/
wget http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift/phylosift_latest.tar.bz2
tar xjf phylosift_latest.tar.bz2
rm phylosift_latest.tar.bz2
mv phylosift_* ~/programs/phylosift
export PATH="$HOME/programs/phylosift":$PATH

# Databases #
mkdir -p ~/share/phylosift
cd ~/share/phylosift
wget http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift_markers/markers.tgz
wget http://edhar.genomecenter.ucdavis.edu/~koadman/ncbi.tgz
tar xzf markers.tgz
tar xzf ncbi.tgz
rm ncbi.tgz
rm markers.tgz

# Run a test example #
cd ~/repos/examples/phylosift
rm -rf results
phylosift all --output=results contig.fasta

The output was the following:

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.
rm: cannot remove `~/repos/examples/phylosift/results/blastDir/*.aa.1*': No such file or directory
xapple@server phylosift $ echo $?
0
xapple@server phylosift $

Even though the exit code of the command was 0. Should I be worried ?

koadman commented 9 years ago

The error message is popping up because phylosift wasn't able to find any marker gene homologs in your dataset. Probably the results are empty too. It's not a very informative error message -- this is something that could be improved.

mkroege1 commented 8 years ago

I have the same issue. This is the debug output: user@Puget-145815:~/phylosift_v1.0.1$ phylosift all -f --paired tutorial_data/HMP_1.fastq.gz tutorial_data/HMP_2.fastq.gz --debug READSFILE tutorial_data/HMP_1.fastq.gz 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 2016-03-07 10:01:40 All systems are good to go, continuing the screening deleting an old run /home/user/phylosift_v1.0.1/PS_temp/HMP_1.fastq.gz MODE : all Using updated markers Using a marker list file /home/user/share/phylosift/markers/marker_list.txt Before runBlast 2016-03-07 10:01:41 USING 0 Input type is dna, fastq Making fifos Launching search process 1 Running /home/user/phylosift_v1.0.1/bin/lastal -F15 -e75 -f0 /home/user/share/phylosift/markers/replast "/home/user/phylosift_v1.0.1/PS_temp/HMP_1.fastq.gz/blastDir/last_0.pipe" |Opening /home/user/phylosift_v1.0.1/PS_temp/HMP_1.fastq.gz/blastDir/reads.fasta.1 Octopus is handing out sequences Octopus handed out 7772 sequences Writing candidates from process 1 ReadsFile: tutorial_data/HMP_1.fastq.gz .lastal Got 0 markers with hits .lastal Got 0 nucleotide markers with hits After runBlast 2016-03-07 10:01:41 Before runAlign 2016-03-07 10:01:41 after marker prep AFTER ALIGN and MASK Using a marker list file /home/user/share/phylosift/markers/marker_list.txt Using a marker list file /home/user/share/phylosift/markers/marker_list.txt AFTER concatenateALI After runAlign 2016-03-07 10:01:41 Before runPplacer 2016-03-07 10:01:41 After runPplacer 2016-03-07 10:01:41 Before runSummarize 2016-03-07 10:01:41

**STARTING SUMMARY

Writing sequences Total classifiable probability mass is 0 Before runKrona 2016-03-07 10:01:41 Generating krona After runKrona 2016-03-07 10:01:41 Debug lvl : 1 After runBlast 2016-03-07 10:01:41 MODE :: all After START 2016-03-07 10:01:41

gjospin commented 8 years ago

Has the reference database been downloaded? It should be in /home/user/share/phylosift/markers

If that directory does not exists then you might need to manually download the references from http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift_markers/markers.tgz

and unpack the archive in /home/user/share/phylosift/

Once that's been done, you might need to index the database before running phylosift.

phylosift index

I hope this helps.

On Mon, Mar 7, 2016 at 7:14 AM, mkroege1 notifications@github.com wrote:

I have the same issue. This is the debug output: user@Puget-145815:~/phylosift_v1.0.1$ phylosift all -f --paired tutorial_data/HMP_1.fastq.gz tutorial_data/HMP_2.fastq.gz --debug READSFILE tutorial_data/HMP_1.fastq.gz 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 2016-03-07 10:01:40 All systems are good to go, continuing the screening deleting an old run /home/user/phylosift_v1.0.1/PS_temp/HMP_1.fastq.gz MODE : all Using updated markers Using a marker list file /home/user/share/phylosift/markers/marker_list.txt Before runBlast 2016-03-07 10:01:41 USING 0 Input type is dna, fastq Making fifos Launching search process 1 Running /home/user/phylosift_v1.0.1/bin/lastal -F15 -e75 -f0 /home/user/share/phylosift/markers/replast "/home/user/phylosift_v1.0.1/PS_temp/HMP_1.fastq.gz/blastDir/last_0.pipe" |Opening /home/user/phylosift_v1.0.1/PS_temp/HMP_1.fastq.gz/blastDir/reads.fasta.1 Octopus is handing out sequences Octopus handed out 7772 sequences Writing candidates from process 1 ReadsFile: tutorial_data/HMP_1.fastq.gz .lastal Got 0 markers with hits .lastal Got 0 nucleotide markers with hits After runBlast 2016-03-07 10:01:41 Before runAlign 2016-03-07 10:01:41 after marker prep AFTER ALIGN and MASK Using a marker list file /home/user/share/phylosift/markers/marker_list.txt Using a marker list file /home/user/share/phylosift/markers/marker_list.txt AFTER concatenateALI After runAlign 2016-03-07 10:01:41 Before runPplacer 2016-03-07 10:01:41 After runPplacer 2016-03-07 10:01:41 Before runSummarize 2016-03-07 10:01:41

**STARTING SUMMARY

Writing sequences Total classifiable probability mass is 0 Before runKrona 2016-03-07 10:01:41 Generating krona After runKrona 2016-03-07 10:01:41 Debug lvl : 1 After runBlast 2016-03-07 10:01:41 MODE :: all After START 2016-03-07 10:01:41

— Reply to this email directly or view it on GitHub https://github.com/gjospin/PhyloSift/issues/466#issuecomment-193292921.

mkroege1 commented 8 years ago

So I had already downloaded the markers.tgz and ncbi.tgz and unpacked it into phylosift directory. I have now run the command you stated above to index the database, but it is still having the same error. Any other ideas?

kstangline commented 3 years ago

Bump. I'm having the same error as above.