When I run python VIBRANT_setup.py or download-db.sh to download the required database, I always get this error:
/gss1/home/zhenggy01/app/miniconda3/envs/vibrant/bin/download-db.sh:17: /etc/conda/activate.d/vibrant.sh: No such file or directory exists.
/gss1/home/zhenggy01/app/miniconda3/envs/vibrant/bin/download-db.sh:21: /etc/conda/deactivate.d/vibrant.sh: No such file or directory exists.
tar (child): vog.hmm.tar.gz:can not open: No such file or directory exists.
tar (child): Error is not recoverable: exiting now
tar (child): profiles.tar.gz:can not opentar: Child returned status 2
: No such file or directory exists.ar:
Error is not recoverable: exiting nowtar (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: VOG*.hmm: No such file or directory exists.
cat: profiles/K*.hmm: No such file or directory exists.
rm: can not delete "VOG0*.hmm": No such file or directory exists.
rm: can not delete"VOG1*.hmm"rm: : No such file or directory exists."VOG2*.hmm"
: No such file or directory exists
rm: can not delete"profiles": No such file or directory exists
Error: File format problem in trying to open HMM file vog_temp.HMM.
File exists, but appears to be empty?
Error: File format problem in trying to open HMM file kegg_temp.HMM.
File exists, but appears to be empty?
rm: can not delete"vog.hmm.tar.gz": No such file or directory exists
rm: can not delete"profiles.tar.gz": No such file or directory exists
mv: can not get"Pfam-A.hmm" (stat): No such file or directory exists
Error:
Error:
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)
File existence/permissions problem in trying to open HMM file VOGDB94_phage.HMM.
HMM file VOGDB94_phage.HMM not found (nor an .h3m binary of it)
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: /gss1/home/zhenggy01/database/vibrant/databases/KEGG_profiles_prokaryotes.HMM: No such file or directory exists
/gss1/home/zhenggy01/app/miniconda3/envs/vibrant/lib/python3.8/site-packages/sklearn/utils/multiclass.py:13: DeprecationWarning: Please use spmatrix from the scipy.sparse namespace, the scipy.sparse.base namespace is deprecated.
from scipy.sparse.base import spmatrix
Traceback (most recent call last):
File "VIBRANT_setup.py", line 227, in
listing_shell = subprocess.check_output(listing, shell=True)
File "/gss1/home/zhenggy01/app/miniconda3/envs/vibrant/lib/python3.8/subprocess.py", line 415, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/gss1/home/zhenggy01/app/miniconda3/envs/vibrant/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'grep -c "NAME" /gss1/home/zhenggy01/database/vibrant/databases/KEGG_profiles_prokaryotes.HMM' returned non-zero exit status 2.
When I run python VIBRANT_setup.py or download-db.sh to download the required database, I always get this error:
/gss1/home/zhenggy01/app/miniconda3/envs/vibrant/bin/download-db.sh:17: /etc/conda/activate.d/vibrant.sh: No such file or directory exists.
/gss1/home/zhenggy01/app/miniconda3/envs/vibrant/bin/download-db.sh:21: /etc/conda/deactivate.d/vibrant.sh: No such file or directory exists.
tar (child): vog.hmm.tar.gz:can not open: No such file or directory exists.
tar (child): Error is not recoverable: exiting now
tar (child): profiles.tar.gz:can not opentar: Child returned status 2
: No such file or directory exists.ar:
Error is not recoverable: exiting nowtar (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: VOG*.hmm: No such file or directory exists.
cat: profiles/K*.hmm: No such file or directory exists.
rm: can not delete "VOG0*.hmm": No such file or directory exists.
rm: can not delete"VOG1*.hmm"rm: : No such file or directory exists."VOG2*.hmm"
: No such file or directory exists
rm: can not delete"profiles": No such file or directory exists
Error: File format problem in trying to open HMM file vog_temp.HMM.
File exists, but appears to be empty?
Error: File format problem in trying to open HMM file kegg_temp.HMM.
File exists, but appears to be empty?
rm: can not delete"vog.hmm.tar.gz": No such file or directory exists
rm: can not delete"profiles.tar.gz": No such file or directory exists
mv: can not get"Pfam-A.hmm" (stat): No such file or directory exists
Error:
Error:
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)
File existence/permissions problem in trying to open HMM file VOGDB94_phage.HMM.
HMM file VOGDB94_phage.HMM not found (nor an .h3m binary of it)
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: /gss1/home/zhenggy01/database/vibrant/databases/KEGG_profiles_prokaryotes.HMM: No such file or directory exists
/gss1/home/zhenggy01/app/miniconda3/envs/vibrant/lib/python3.8/site-packages/sklearn/utils/multiclass.py:13: DeprecationWarning: Please use
spmatrixfrom thescipy.sparsenamespace, thescipy.sparse.basenamespace is deprecated.from scipy.sparse.base import spmatrix
Traceback (most recent call last):
File "VIBRANT_setup.py", line 227, in
listing_shell = subprocess.check_output(listing, shell=True)
File "/gss1/home/zhenggy01/app/miniconda3/envs/vibrant/lib/python3.8/subprocess.py", line 415, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/gss1/home/zhenggy01/app/miniconda3/envs/vibrant/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'grep -c "NAME" /gss1/home/zhenggy01/database/vibrant/databases/KEGG_profiles_prokaryotes.HMM' returned non-zero exit status 2.