Phylophlan_metagenomic.py

[wangjianing0618]

Hi, Thank you for this useful tool.

I got errors using phylophlan_metagenomic.py as follows: phylophlan_metagenomic -i test -d SGB.Dec19 -o test-out --nproc 4 -n 10

The error details: Traceback (most recent call last): File "/home/wjn/.conda/envs/phylophlan/bin/phylophlan_metagenomic", line 10, in sys.exit(phylophlan_metagenomic()) File "/home/wjn/.conda/envs/phylophlan/lib/python3.8/site-packages/phylophlan/phylophlan_metagenomic.py", line 884, in phylophlanmetagenomic f.write('\t'.join([binn] + ["{}{}:{}:{}:{}".format(sgb_2_info[i[0]][5], File "/home/wjn/.conda/envs/phylophlan/lib/python3.8/site-packages/phylophlan/phylophlanmetagenomic.py", line 884, in f.write('\t'.join([binn] + ["{}{}:{}:{}:{}".format(sgb_2_info[i[0]][5], KeyError: '54917'

The attached file is the log.

Many thanks, Jianing Wang

[wangjianing0618]

test.log

[fasnicar]

Hi, many thanks for reporting this. We had some problems with the Dec19 SGB release and it is now not among the ones available until the final version has been fixed.

Can you run:

phylophlan_metagenomic --database_update

This will update the available database and the latest is now SGB.Nov19.

Then, can you re-run your phylophlan_metagenomic using the SGB.Nov19 database?

phylophlan_metagenomic -i test -d SGB.Nov19 -o test-out2 --nproc 4 -n 10 --verbose

Please, notice that I changed the output folder to test-out2 to avoid that previous file can cause problems with the new run.

Many thanks, Francesco

[wangjianing0618]

Thank you for your reply. Actually, I can't download and update the database directly because of unavailable network connection to google dropbox, I just copied the SGB.Dec19 from my partner. So, do you have any other ways to get the latest database now?

Best wishes, Jianing Wang

[fasnicar]

Hi, I see. Unfortunately, I have the database available only through Dropbox at the moment. These are the URLs of the 3 files needed for the latest db (SGB.Nov19):

• https://www.dropbox.com/s/68i0ddwoonhwzu1/SGB.Nov19.md5?dl=1
• https://www.dropbox.com/s/bvrz4zpt3538ct0/SGB.Nov19.tar?dl=1
• https://www.dropbox.com/s/zzo95dpfhq3n0h8/SGB.Nov19.txt.bz2?dl=1

Can you ask someone to download the for you if you can't download from Dropbox?

Thanks, Francesco

[wangjianing0618]

I see, thank you very much for your help.

[fasnicar]

Hi Jianing Wang, I just wanted to follow up on this. I now moved the databases to https://zenodo.org/ and I'm updating the Bioconda package to be able to download from the new location. I hope this should fix the Dropbox problem.

Many thanks, Francesco

[wangjianing0618]

This is really good news. Thank you very much for your understanding and support.

Best wishes, Jianing Wang