Has someone experience with the KOBAS (v. 3) standalone enrichment software?
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Entering edit mode
16 months ago
t.bergmann • 0

Hello everyone, since I am working with a lot of NGS data for which I want to perform KEGG enrichment analysis I tried to get the standalone version of KOBAS 3 to work on my workstation. So far, most features are running but I have one problem with the "annotate.py" script. If I want to annotate fasta-files I always get the following error message:

"IOError: Bad fasta format at ' the FIRST ' sequence" (from the fasta.py script in KOBAS)

However, if I start the script with ENSEMBL or UniprotIDs, everything works fine. I checked the scripts but could not figure out why the software does not recognize the fasta-files. I tried several different fasta-files (also downloaded some from NCBI) and also tested those with a custom-written biopython script. My script was able to read in the fasta-files with no error messages. So I am clueless. The documentation of the KOBAS package is rather simple and I also could not find any solutions on the internet. So I was wondering if anybody else has experience with the standalone version of KOBAS and might be able to help me! Thanks in advance!

KOBAS enrichment standalone biopython kegg • 724 views
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Entering edit mode
8 months ago

Hi, have you solve this error yet? I also have it. Tried with multiple fasta files and had the same error even with the example.fasta from the software...

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6 months ago

Hi, guys. I suggest that you can install KOBAS docker image to run analyses. I also met this error, but failed to solve. Therefore I installed Docker image of KOBAS, it run successfully, even for fasta file. https://zhuanlan.zhihu.com/p/344760062 if you can understand Chinese, you can install following this.

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Is it downloadable for you now. This docker is not downloadable now. Do you have any alternative source. The kobas webserver is down for 1 week :(

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