Not all files transferred during git clone, or bioconda install

[reesea22]

First, thank you for the very easy to follow installation instructions!

I am receiving the following errors when trying to run VIBRANT_setup.py after installing VIBRANT in a conda environment (bioconda and git clone also did not work for me).

python3 databases/VIBRANT_setup.py

This script will download, extract subsets and press HMM profiles for VIBRANT. This process will require ~20GB of temporary free storage space, but the final size requirement is ~11GB in the form of pressed HMM databases. Please be patient. This only needs to be run once and will take a few minutes. Logger started. Check log file for messages and errors. tar (child): profiles.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now gzip: Pfam-A.hmm.gz: No such file or directory tar: Child returned status 2 tar: Error is not recoverable: exiting now cat: profiles/K*.hmm: No such file or directory rm: cannot remove ‘profiles’: No such file or directory

Error: Failed to open key file profile_names/VIBRANT_vog_profiles.txt

Error: File format problem in trying to open HMM file kegg_temp.HMM. File exists, but appears to be empty?

mv: cannot stat ‘Pfam-A.hmm’: No such file or directory rm: cannot remove ‘profiles.tar.gz’: No such file or directory

Error: File format problem in trying to open HMM file VOGDB94_phage.HMM. File exists, but appears to be empty?

Error: File existence/permissions problem in trying to open HMM file KEGG_profiles_prokaryotes.HMM. HMM file KEGG_profiles_prokaryotes.HMM not found (nor an .h3m binary of it)

Error: File existence/permissions problem in trying to open HMM file Pfam-A_v32.HMM. HMM file Pfam-A_v32.HMM not found (nor an .h3m binary of it)

grep: VIBRANT-1.2.1/databases/KEGG_profiles_prokaryotes.HMM: No such file or directory Traceback (most recent call last): File "databases/VIBRANT_setup.py", line 229, in listing_shell = subprocess.check_output(listing, shell=True) File "/VIBRANT/lib/python3.8/subprocess.py", line 415, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/VIBRANT/lib/python3.8/subprocess.py", line 516, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'grep -c "NAME" /VIBRANT-1.2.1/databases/KEGG_profiles_prokaryotes.HMM' returned non-zero exit status 2

[KrisKieft]

Hi,

My first guess is that something appears to be wrong with wget of the HMM profiles. This error is harder to troubleshoot because I had a lot of wget outputs be hidden. Can you trying just typing wget on the command line and ensure you have it installed?

[jowodo]

I had some similar problem: have you tried doing it manually (issue #39)? This worked for me. The databases directory is stored in $VIBRANT_DATA_PATH which is for me under /apps/vibrant/1.2.1/share/vibrant-1.2.1/db. From within this databases directory following the instructions from #39 did the trick. I hope this helps anyone facing the same problem.

[rotoscan]

Hello,

I had the same issue.

I followed the thread on issue #39 but I got the same problem. On step 5: hmmfetch -o VOGDB94_phage.HMM -f vog_temp.HMM profile_names/VIBRANT_vog_profiles.txt

It expects this file to exist, but it is not there...

Any help is appreciated, I would really like to use this tool! =)

Best, Rodolfo

[jowodo]

@rotoscan if VIBRANT_run.py is in your $PATH, then this command should give you the location of VIBRATN_vog_profiles.txt if you've installed with conda install -c bioconda vibrant==1.2.1: readlink -f $(dirname $(which VIBRANT_run.py ))/../share/vibrant-1.2.1/db/databases/profile_names/VIBRANT_vog_profiles.txt with the according version number of course

[rotoscan]

That worked!

thanks a lot @pur80a !

[decrevi]

I recently had this same issue. It is due to wget not downloading the files from the two FTP sites. I ended up downloading the files manually (using Chrome) and putting the files in the databases folder. Then I commented out the lines to download the files (mainly for speed, since wget waits a LONG time for it to time out), and ran the VIBRANT_setup.py . That seems to have fixed the issue. It would be good to fix the wget issue though, maybe that is due to server upgrades or wget version?