Vibrant now working - Githubissues

Encountered an error and have tried it multiple times

Below are the error messsage;

Downloading VIBRANT databases to /home/priscilla/anaconda3/envs/vibrant/share/vibrant-1.0.1...

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 ~11.2GB in the form of pressed HMM databases. Please be patient. This only needs to be run once and will take a few minutes.

Verifying Pfam, KEGG and VOG source websites are available for download ...

Downloading HMM profiles for Pfam, KEGG and VOG from their source websites ... 2022-12-20 17:05:55 (350 KB/s) - Data connection: Connection timed out; Data transfer aborted. 2022-12-20 17:20:31 (166 KB/s) - Data connection: Connection timed out; Data transfer aborted. Aborted (core dumped) 2022-12-20 17:52:16 (121 KB/s) - Data connection: Connection timed out; Data transfer aborted. 2022-12-20 18:07:31 URL:https://fileshare.csb.univie.ac.at/vog/vog94/vog.hmm.tar.gz [329720997/329720997] -> "vog.hmm.tar.gz" [3] 2022-12-20 18:25:21 (16.8 KB/s) - Data connection: Connection timed out; Data transfer aborted. 2022-12-20 18:44:57 (23.4 KB/s) - Data connection: Connection timed out; Data transfer aborted. 2022-12-20 19:04:45 (41.0 KB/s) - Data connection: Connection timed out; Data transfer aborted. 2022-12-20 19:26:27 (35.0 KB/s) - Data connection: Connection timed out; Data transfer aborted. 2022-12-20 19:46:03 (36.0 KB/s) - Data connection: Connection timed out; Data transfer aborted. Error in server response, closing control connection. 2022-12-20 20:14:53 (33.2 KB/s) - Data connection: Connection timed out; Data transfer aborted. Aborted (core dumped)

Unzipping profiles ...

gzip: Pfam-A.hmm.gz: unexpected end of file

gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now

Concatenating individual profiles ...

Extracting profiles used for VIBRANT ...

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

Error: bad file format in HMM file kegg_temp.HMM

Retrieved 19182 HMMs. mv: cannot stat 'Pfam-A.hmm': No such file or directory

Pressing profiles used for VIBRANT ...

Error: Working... File existence/permissions problem in trying to open HMM file Pfam-A_plasmid_v32.HMM. HMM file Pfam-A_plasmid_v32.HMM not found (nor an .h3m binary of it)

Working...
Error: File existence/permissions problem in trying to open HMM file Pfam-A_phage_v32.HMM. HMM file Pfam-A_phage_v32.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)

done. Pressed and indexed 3048 HMMs (3048 names). Models pressed into binary file: KEGG_profiles_prokaryotes.HMM.h3m SSI index for binary model file: KEGG_profiles_prokaryotes.HMM.h3i Profiles (MSV part) pressed into: KEGG_profiles_prokaryotes.HMM.h3f Profiles (remainder) pressed into: KEGG_profiles_prokaryotes.HMM.h3p done. Pressed and indexed 19182 HMMs (19182 names). Models pressed into binary file: VOGDB94_phage.HMM.h3m SSI index for binary model file: VOGDB94_phage.HMM.h3i Profiles (MSV part) pressed into: VOGDB94_phage.HMM.h3f Profiles (remainder) pressed into: VOGDB94_phage.HMM.h3p

Done. Several new databases are now in this folder.

VIBRANT should be ready to go. You can verify this by running VIBRANT_test_setup.py within this folder (databases/)

Testing VIBRANT databases... grep: /home/priscilla/anaconda3/envs/vibrant/share/vibrant-1.0.1/databases/Pfam-A_phage_v32.HMM: No such file or directory Traceback (most recent call last): File "/home/priscilla/anaconda3/envs/vibrant/share/vibrant-1.0.1/databases/VIBRANT_test_setup.py", line 49, in listing_shell = subprocess.check_output(listing, shell=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/priscilla/anaconda3/envs/vibrant/lib/python3.11/subprocess.py", line 465, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/priscilla/anaconda3/envs/vibrant/lib/python3.11/subprocess.py", line 569, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'grep -c "NAME" /home/priscilla/anaconda3/envs/vibrant/share/vibrant-1.0.1/databases/Pfam-A_phage_v32.HMM' returned non-zero exit status 2. VIBRANT databases are downloaded successfully.

replikation / What_the_Phage

Vibrant now working #179