NCBI taxonomy data file missing

[Josiah Wagner]

Hi all,

Yesterday I obtained PhyloSift from Git and manually installed the Markers database from the updated link (https://figshare.com/articles/PhyloSift_markers_database/5755404/1).

However, I can't figure out how to manually install the NCBI taxonomy data since the http://edhar.genomecenter.ucdavis.edu/~koadman/ncbi.tgz is unavailable.  

So after running:

./phylosift all --paired tutorial_data/HMP_1.fastq.gz tutorial_data/HMP_2.fastq.gz

I get the error:

NCBI taxonomy data not found and unable to connect to update server, please check your phylosift configuration and internet connection!

On another post here, it was suggested taxonomy data could be obtained from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/ but I am unsure which of those files PhyloSift requires in the share/phylosift/ncbi folder.

Thank you for any help!

Sincerely,

Josiah

[Guillaume Jospin]

I did forget to add the ncbi part... I'll see about fixing that. Thanks for pointing it out.

You need the following files in the ncbi directory you mention.

delnodes.dmp

merged.dmp

nodes.dmp

names.dmp

Sorry about the misleading information.

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[Guillaume Jospin]

For some reason the link you share only shows the markers archive.

The ncbi archive is showing when using the following link:

https://figshare.com/articles/PhyloSift_markers_database/5755404

[Josiah Wagner]

Fixed, thanks so much.

Josiah

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[Morgan Sobol]

Hello, 

I followed the guidance below but I am still receiving the error "NCBI taxonomy data not found and unable to connect to update server, please check your phylosift configuration and internet connection!" error.  

The NCBI folder is stored in my phylosift_v1.0.1 directory and contains delnodes.dmp, merged.dmp, nodes.dmp, names.dmp.

I also changed the ncbi directory path in the phylosiftrc file to this directory:

$marker_path="";

# $ncbi_path="";

# $marker_dir="/work/Geomicrobiology/msobol/bin/phylosift_v1.0.1/markers/";

# $markers_extended_dir="";

# $ncbi_dir = "work/Geomicrobiology/msobol/bin/phylosift_v1.0.1/ncbi/";

$marker_base_url = "";

$ncbi_url = "";

Can you please help me?

Thanks,

Morgan S. 

On Thursday, January 18, 2018 at 2:21:03 PM UTC-6, Guillaume Jospin wrote:

I did forget to add the ncbi part... I'll see about fixing that. Thanks for pointing it out.

You need the following files in the ncbi directory you mention.

delnodes.dmp

merged.dmp

nodes.dmp

names.dmp

Sorry about the misleading information.

On Thu, Jan 18, 2018 at 12:09 PM, Josiah Wagner <jtw...@gmail.com> wrote:

Hi all,

Yesterday I obtained PhyloSift from Git and manually installed the Markers database from the updated link (https://figshare.com/articles/PhyloSift_markers_database/5755404/1).

However, I can't figure out how to manually install the NCBI taxonomy data since the http://edhar.genomecenter.ucdavis.edu/~koadman/ncbi.tgz is unavailable.  

So after running:

./phylosift all --paired tutorial_data/HMP_1.fastq.gz tutorial_data/HMP_2.fastq.gz

I get the error:

NCBI taxonomy data not found and unable to connect to update server, please check your phylosift configuration and internet connection!

On another post here, it was suggested taxonomy data could be obtained from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/ but I am unsure which of those files PhyloSift requires in the share/phylosift/ncbi folder.

Thank you for any help!

Sincerely,

Josiah

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[Guillaume Jospin]

Can you try removing the # at the beginning of the lines of interest please?

So in front of $marker_dir and $ncbi_dir

[Morgan Sobol]

Thanks for the quick reply! I feel dumb for not seeing that earlier. Thank you!

It fixed the NCBI error message, but now I am getting this one:

Use of uninitialized value $timestamp in scalar chomp at /work/Geomicrobiology/msobol/bin/phylosift_v1.0.1/bin/../lib/Phylosift/Utilities.pm line 365, <$FH> line 1.

Usage: my $f = File::NFSLock->new('/pathtofile/file',

'BLOCKING|EXCLUSIVE|NONBLOCKING|SHARED', [blocking_timeout, stale_lock_timeout]);

(You passed "" and "2") at /work/Geomicrobiology/msobol/bin/phylosift_v1.0.1/bin/../lib/Phylosift/Utilities.pm line 632.

I can open a new post if need be.

[Guillaume Jospin]

Ah yes, it might be due to the failed earlier PS runs. You might need to manually remove files with the word LOCK in them.

I assume you have write permission to the database directory? Sometimes if you are using a shared DB it can be a bit problematic.

So from your earlier post, I would look in /work/Geomicrobiology/msobol/bin/phylosift_v1.0.1/
Maybe inside markers as well.

[Morgan Sobol]

Would lock be in the file name? If so, I am not finding anything like that. 

[Morgan Sobol]

I fixed it by uninstalling and reinstalling the program.

Thanks!

[Guillaume Jospin]

Oh good. Sorry I forgot to get back to this thread yesterday. 

Thanks for sharing the fix. 

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