Blast results missing

ifer...@unito.it

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Nov 10, 2016, 10:44:26 AM11/10/16

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Dear Dr. Meren,

I'm using the oligotype pipeline (Oligotyping (version: 2.1)) on my datasets. However since i have blast (PACKAGE_NAME: blast PACKAGE_VERSION: 2.2.31) correctly installed in a central position on my mac when i'm running the pipeline i did not obtain the blast result of my oligotype.

I'm using this script

oligotype seq_nogap_acinetobacter.fna seq_nogap_acinetobacter.fna-ENTROPY -C 32,110,244,268,124,241,111,242,230,290,387,125,109,299,30,35,341 -M 50 -A 500 -a 1 -T -N 8 --do-blast-search

Any suggestion?

Ilario

A. Murat Eren

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Nov 10, 2016, 10:46:22 AM11/10/16

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Are there any errors in the log file (which should be in the output directory)?

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A. Murat Eren (meren)
http://merenlab.org :: gpg

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ifer...@unito.it

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Nov 10, 2016, 10:51:00 AM11/10/16

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Here the log file but i did not seen any error

Il giorno giovedì 10 novembre 2016 16:46:22 UTC+1, A. Murat Eren ha scritto:

Are there any errors in the log file (which should be in the output directory)?

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A. Murat Eren (meren)
http://merenlab.org :: gpg

On Thu, Nov 10, 2016 at 9:44 AM, <ifer...@unito.it> wrote:

Dear Dr. Meren,
I'm using the oligotype pipeline (Oligotyping (version: 2.1)) on my datasets. However since i have blast (PACKAGE_NAME: blast PACKAGE_VERSION: 2.2.31) correctly installed in a central position on my mac when i'm running the pipeline i did not obtain the blast result of my oligotype.

I'm using this script

oligotype seq_nogap_acinetobacter.fna seq_nogap_acinetobacter.fna-ENTROPY -C 32,110,244,268,124,241,111,242,230,290,387,125,109,299,30,35,341 -M 50 -A 500 -a 1 -T -N 8 --do-blast-search

Any suggestion?

Ilario

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RUNINFO.log

A. Murat Eren

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Nov 10, 2016, 10:54:04 AM11/10/16

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Hmm. It may be due to the NCBI service, or your internet connection. I suggest once you finalize your oligotypes, analyze the representative sequences outside of the pipeline.

Best,

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A. Murat Eren (meren)
http://merenlab.org :: gpg

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ifer...@unito.it

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Nov 11, 2016, 11:13:46 AM11/11/16

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I thinks it does not working because NCBI switch the IP address (from http to https) If you will fix it the script please let me know

Ilario

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