All Tormes Fixes I have Found in one place. about tormes HOT 7 CLOSED

Hi All, another fix for one of the packages that gives you grief sometimes.

If you are getting errors with tbl2asn try installing: tbl2asn-forever
so,
conda install -c bioconda tbl2asn-forever

it will install libfaketime and tbl2asn-forever

enjoy

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This post is simply GREAT!
Thanks a lot for your efforts summarizing the main issues and how to overcome them! I think this is going to be really useful for other users.
All the best,
Narciso

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Hi,
I am just running my first run, looks good!
About the MAUVE errors:

1. I did the first and second fixes above, but still got an error
2. What downstream analysis use MAUVE output? What further errors are expected or which analysis will be affected?
3. I did not save the error log so I'll try to run it again just to reproduce the error and post
   Best,
   SB

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Hi @shlomobl

1. Indeed, there are some problems when running Mauve in certain systems. Have you tried to run Mauve in the command line without tormes?
2. Mauve output will be the draft genomes ordered against the reference you provided and will be used for downstream analysis. However, if you don't enable Mauve (do not add any reference with the --reference option), the "unordered" genomes will be used instead and the results will not change. The ordering sometimes facilitates comparisons between genomes using graphical interfaces (such as Mauve or Artemis) and that's why I included it in tormes. Summarizing, try to run tormes without the --reference option and let's see what happens.
   Best,
   Narciso

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Hi Brad,

Thanks for the update! I've never tried to update tbl2asn by using that way.
Indeed, there's an issue with that software, as it got outdated yearly and thus stop working.
If you try to update it by its regular conda channel ( conda install -c bioconda tbl2asn ), sometimes still returns an error (as the version recognizes that is more than one year old).

Another option to get tbl2asn updated, is to regularly download it from its NCBI ftp repository (ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/) and replace this new one with the old tbl2asn that is installed in the tormes environment (you can find its location in your system by typing which tbl2asn ).

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Hi
i have problems with quast-download-busco; tormes version 1.3.0 (This is a bug to be fixed in future versions, but I think it's a QUAST problem.)

I cant download busco database. The bug is in this file run_busco.py

ablab/quast#124

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Hi @Panchastico
Indeed, some URLs might have changed in the latest QUAST versions (TORMES was tested and uses QUAST v5.0.2). It is not a TORMES issue and running it without BUSCO won't affect TORMES functionality ;)
We are preparing a major release that will cover this issue.

In the meantime, you can try to download the files manually and place them in their correct path. I can help you with that. Just run:

conda activate tormes-1.3.0

#augustus
wget -O $(which tormes | sed "s/tormes$//")../lib/python3.6/site-packages/quast_libs/augustus3.2.3/augustus.tar.gz http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz
tar xzvf $(which tormes | sed "s/tormes$//")../lib/python3.6/site-packages/quast_libs/augustus3.2.3/augustus.tar.gz

#bacteria
wget -O $(which tormes | sed "s/tormes$//")../lib/python3.6/site-packages/quast_libs/busco/bacteria.tar.gz http://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz

#eukaryota
wget -O $(which tormes | sed "s/tormes$//")../lib/python3.6/site-packages/quast_libs/busco/eukaryota.tar.gz https://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz

#fungi
wget -O $(which tormes | sed "s/tormes$//")../lib/python3.6/site-packages/quast_libs/busco/fungi.tar.gz https://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz

Now, you might be able to use BUSCO functionality with QUAST in TORMES ;)

Let me know if it worked!
Narciso

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