xmao / kobas Goto Github PK

I am facing the following problem:
python3 blast2ko.py -p longest_isoform_cdhit_trinity_GKTrinity.fasta
File "/media/bioinfo/hdd1/Afsana_Hilsa/Hilsa_osmoregulation_old/All_fasta_trinity_cdhit_longest/blast2ko.py", line 69
except exception.FastaIOError, msg:
^
SyntaxError: invalid syntax

How can i fix it?
thanks in advance.

I am using KOBAS 3 webserver to analysis my DEGs, i uploaded my protein.fasta file to KOBAS 3 webserver.
However, the status of task is "Your task is in the queue" for 2 days, and no result is load. It is unusual.
My task link is http://kobas.cbi.pku.edu.cn/retrieve/?taskid=cf28cca17314408cbe8709d132a8cd13.

Can you help me to check it.
Thanks.

Hi,

I would like to annotate a species of Fusarium. But on the website, there are only three species. So I would like to know whether I can use this software to annotate the genome. And which species should I select?
Thank you in advance.

Hello kobas Team,
We run kobas (annotate.py) on our cluster, however we keep getting the following error "Error: configuration file does not exist."
We are wondering what could be the problem.
Thank you,
Robert

Dear xamao,

I was trying to reach and use KOBAS 3 webserver (http://kobas.cbi.pku.edu.cn/kobas3/?t=1) but the server is not responding. Would it be possible to look into this issue?

Thank you very much

Best Regards
Ahmad

Hello,

Thank you for creating such a convenient tool for enrichment analysis.

However, I encountered a problem when performing KEGG pathway enrichment analysis of differentially expressed genes in rice. Since the web version has limitations on the number of genes, I ran the analysis locally using KOBAS installed on the school cluster. I was able to run the human example data successfully.

The first step was annotation. Since the local version does not support id:gene_symbol (my gene name example: Os10g0497300), I chose to annotate online (Plants / Monocots / Oryza sativa japonica (Japanese rice)(RAPDB)), resulting in the file: anno_seq.tsv. The file anno_seq.tsv was downloaded from kobas website.

The second step was to run the identification command, which resulted in an error.
identify.py -f anno_seq.tsv -o identifyout -q /public/home/wyang/biosofts/kobas/ftp.cbi.pku.edu.cn/pub/KOBAS_3.0_DOWNLOAD/sqlite3 -y /public/home/wyang/biosofts/kobas/ftp.cbi.pku.edu.cn/pub/KOBAS_3.0_DOWNLOAD/seq_pep

Traceback (most recent call last):
File "/public/home/software/opt/bio/software/kobas/3.0//scripts/identify.py", line 3, in
from kobas.scripts import identify
File "/public/home/software/opt/bio/software/kobas/3.0/src/kobas/scripts/identify.py", line 189, in
bdistr = discover.distr_from_default(opt.bgfile, db, speciesdb, abbr, opt.cutoff, idmapping)
File "/public/home/software/opt/bio/software/kobas/3.0/src/kobas/discover.py", line 119, in distr_from_default
dblink_ids = [dblink_id[0] for dblink_id in speciesdb.dblink_ids_from_gid(gid['gid'], idmapping)]
TypeError: 'NoneType' object is not iterable

How can I solve this issue? We will actively cite such a convenient software!

I used diamond for speeding up blastx alignment of .fasta file to hsa.pep.fasta from kobas.cbi.pku.edu.cn/download/, then I tried to use annotate.py to annotate, and this error message appears:

Error message:
Bad blastout format. You can choose to input the FASTA file directly (-t fasta:nuc or fasta:pro) or run blast+ locally against FASTA sequence file in the latest backend databases of KOBAS 2.0. Please refer to instructions(http://kobas.cbi.pku.edu.cn/download.do) for details

However, as I tried another species, it ran successfully.

in your docs/install.txt there are some instructions and those were last updated in 2010.
in your contrib/dump.sh there are instructions related to uploading data into database using data dumps. Where are these data dumps?

Your repository was last updated in 2010. i would think that this project has been discontinued. How do i make this work? Would you suggest anyother tool as an alternate for your tool.
i'm not able to access your website also.

请问http://kobas.cbi.pku.edu.cn/这个网址还可以使用吗？为什么每次访问都是拒绝连接呢？