Problems running Phylosift

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kyle catalan

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May 22, 2018, 9:30:05 PM5/22/18
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Hi all,

I have recently downloaded Phylosift from the following link: 


And I've tried executing the workflow for the tutorial. However, when I input the command: 

./phylosift all -f --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.

On another post here, someone had a similar problem and the solution for that was to download the ncbi directory from figshare. So, I've downloaded it in my home directory in the folder "share" but when I try to execute the command for the tutorial, the same error comes up. I've also tried to download the markers for phylosift, but the same error also comes up. How should I proceed?

Thank you for any help.

Regards,

Kyle


Guillaume Jospin

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May 23, 2018, 1:04:00 AM5/23/18
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You should have the following two directories share/phylosift/markers and /share/phylosift/ncbi
That's where phylosift will look for the databases by default.


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kyle catalan

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May 23, 2018, 2:16:22 AM5/23/18
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Initially, I had the ncbi in the share directory. I have now moved it into share/phylosift/

I've just tried the tutorial command again, but I get a new error. Any idea how I could troubleshoot this?

rm: cannot remove '/shared/homes/12016150/phylosift_v1.0.1/PS_temp/HMP_1.fast.gz/blastDir/*.aa.1*': No such file or directory

NB: 12016150 is just my home directory.

On Wednesday, May 23, 2018 at 3:04:00 PM UTC+10, Guillaume Jospin wrote:
You should have the following two directories share/phylosift/markers and /share/phylosift/ncbi
That's where phylosift will look for the databases by default.

On Tue, May 22, 2018 at 6:30 PM, kyle catalan <kyleca...@gmail.com> wrote:
Hi all,

I have recently downloaded Phylosift from the following link: 


And I've tried executing the workflow for the tutorial. However, when I input the command: 

./phylosift all -f --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.

On another post here, someone had a similar problem and the solution for that was to download the ncbi directory from figshare. So, I've downloaded it in my home directory in the folder "share" but when I try to execute the command for the tutorial, the same error comes up. I've also tried to download the markers for phylosift, but the same error also comes up. How should I proceed?

Thank you for any help.

Regards,

Kyle


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Guillaume Jospin

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May 23, 2018, 10:37:43 AM5/23/18
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Can you use the -f flag? It'll start a clean working directory

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kyle catalan

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May 23, 2018, 7:17:25 PM5/23/18
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Yep, I've just tried the -f flag and the same error comes up. However, it does produce the PS_Temp directory and the HMP_1.fastq.gz directory (does not produce the HMP_2.fastq.gz directory)

I believe there are some missing file types though, this is what the HMP_1.fastq.gz directory contained: 

alignDir             run_info.txt                 sequence_taxa.txt

blastDir             sequence_taxa.1.txt          taxa_90pct_HPD.txt

HMP_1.fastq.gz.html  sequence_taxa_summary.1.txt  taxasummary.txt

marker_summary.txt   sequence_taxa_summary.txt    treeDir

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