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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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File/Path Error #1197

Closed fetyj closed 5 years ago

fetyj commented 5 years ago

Hello, I'm trying to get pangenomic analysis for Lactobacillus plantarum from NCBI, then follow the tutorial here (http://merenlab.org/2019/03/14/ncbi-genome-download-magic/#processing-ncbi-genomes) Problem, when I get to that part anvi-run-workflow -w contigs -c contig.json I got this error message 

Config Error: Well, the fasta.txt entry name contains characters that anvi'o does not like :/
              Please limit the characters to ASCII letters, digits, and the underscore ('_') 
              character

So I create a bash file as the example but now I get stuck with this kind of error

sh anvi.sh 
Input FASTA file .............................: /choppy/Lb_plant_anviopan/Lactobacillus_plantarum_16_GCF_000412205.1-contigs.fa
Name .........................................: Lactobacillus_plantarum_16_GCF_000412205.1
Description ..................................: No description is given

File/Path Error: You do not have permission to generate the output file                 
                 '/home/fiestaj/plantarum/Lactobacillus_plantarum_16_GCF_000412205.1.db'

File/Path Error: No such file:                                                             
                 '/home/fiestaj/plantarum/Lactobacillus_plantarum_16_GCF_000412205.1.db' :/

Any help would be great, Thanks,

Fety Anvi-profile

Anvi'o version ...............................: margaret (v5.4)
Profile DB version ...........................: 31
Contigs DB version ...........................: 12
Pan DB version ...............................: 13
Genome data storage version ..................: 6
Auxiliary data storage version ...............: 2
Structure DB version .........................: 1
meren commented 5 years ago

Hi @fetyj,

I am not sure if this error is associated with v5.4 and fixed in v5.5 because we do not have any other complaints about this workflow.

Please consider upgrading your anvi'o version to v5.5 and try again. I apologize for the extra work, but we do not have the human resources to support older versions of anvi'o :)

Best wishes,

fetyj commented 5 years ago

Indeed, upgrading fix it! Thanks for the help :)

AnaValero commented 5 years ago

Hi, First of all, congratulations and thanks for creating such great tool that I'm looking forward to use in my projects.

I'm having the same problem with anvio version 5.5.0 (installed yesterday), using the Spiroplasma data: http://merenlab.org/data/spiroplasma-pangenome/

Once I run the following command: anvi-run-workflow -w pangenomics -c pan-config.json

I get the following error:

Config Error: Well, the fasta.txt entry name contains characters that anvi'o does not like :/ Please limit the characters to ASCII letters, digits, and the underscore ('_') character.

Here is my pan-config.json file after removing the character "-" from Spiroplasma-fasta.txt and leaving as Spiroplasma.txt (same error when using the exact names provided in the tutorial):

{ "fasta_txt": "Spiroplasma.txt", "project_name": "Spiroplasma", "external_genomes": "external_genomes.txt" }

Do I also need to create a sh file? In such a case I have no clue which info it must contain and how to use. Any help would be very much appreciated.

Best regards, Ana

meren commented 5 years ago

Hi @AnaValero,

Here is my pan-config.json file after removing the character "-" from Spiroplasma-fasta.

It is not complaining about characters in the file name. It is complaining about the name column in that file. If you look at the first column of the contents of this file, you should see names that match to what that Config Error says. There is a line in the workflow about that:

image

If nothing makes sense, please send your fasta_txt file.

AnaValero commented 5 years ago

Hi,

Many thanks for your prompt reply. I've been working on the issue and it seems that it was due to the command below, as the added name was "Spiroplasma_MAG.fat". I changed it to "Spiroplasma_MAG" and the issue was solved.

echo -e "Spiroplasma_MAG.fa\tpwd/MAGs/Spiroplasma_MAG.fa" \

Spiroplasma-fasta.txt

Afterwards I got different errors that I solved by setting up the COG distribution (anvi-setup-ncbi-cogs) and running again the workflow. It was then running for 12 hour approximately with no issues.

However, when I tried:

anvi-compute-ani -e external-genomes.txt \ -o ANI \ -p 03_PAN/Spiroplasma-PAN.db \ -T 6

It produced the following error message after being running for a couple of hours:

(anvio5) ana@ana-Not-Specified ~/Desktop/MAGs $ anvi-compute-ani -e external-genomes.txt -o ANI -p 03_PAN/Spiroplasma-PAN.db -T 6

CITATION

Anvi'o will use 'PyANI' by Pritchard et al. (DOI: 10.1039/C5AY02550H) to compute ANI. If you publish your findings, please do not forget to properly credit their work.

[PyANI] Num threads to use ...................: 6 [PyANI] Alignment method .....................: ANIb [PyANI] Log file path ........................: /tmp/tmpicz3jdoj

Genomes found ................................: 34 Temporary FASTA output directory .............: /tmp/tmpc1x6jk25 Output directory .............................: /home/ana/Desktop/MAGs/ANI

[05 Sep 19 10:39:27 PyANI] Running ...

Config Error: PyANI returned with non-zero exit code, there may be some errors. please check the log file for details.

I've tried to find such log file within 00_LOGS folder unsuccessfully. Also, I found in google that a user had the same error due to an old version of python installed in his computer. I have Python 3.6 installed, so I don't believe that it is my case.

Do you have any recommendation? I'm afraid that I got stuck here.

Many thanks!! Ana

El lun., 2 sept. 2019 a las 16:44, A. Murat Eren (notifications@github.com) escribió:

Hi @AnaValero https://github.com/AnaValero,

Here is my pan-config.json file after removing the character "-" from Spiroplasma-fasta.

It is not complaining about characters in the file name. It is complaining about the name column in that file. If you look at the first column of the contents of this file, you should see names that match to what that Config Error says. There is a line in the workflow about that:

[image: image] https://user-images.githubusercontent.com/197307/64122096-4042f900-cd66-11e9-8374-8c03f8e44ac9.png

If nothing makes sense, please send your fasta_txt file.

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