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!
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t.bergmann •
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...
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.
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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