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b-tierney / vironomy

Viral taxonomic classification and phylogenetic trees
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FileNotFoundError: [Errno 2] No such file or directory: 'home/databases/vironomy/vironomy_database//vironomy_database/Genus_single_copy_marker_database.csv' #1

Open Choaro opened 1 year ago

Choaro commented 1 year ago

I successfully installed vironomy and downloaded the database.

Here is the database list:

full_sc_marker_db.csv genbank_pfam_tgirfam_all_annotations_sc.txt genbank_predicted_proteins.faa group_taxid_contigid_mapping_annotation_data.tsv single_copy_marker_database.csv single_copy_marker_db.hmm

I have one fasta file with alll the viral contigs from virsorter2

when I run:

vironomy end_to_end -i Final-dvf-vs-viral_95.fasta -e 1e-5 -d home/databases/vironomy/vironomy_database//vironomy_database -p 20

I get this error message:

(vironomy) [choaro@marvin vironomy_database]$ vironomy end_to_end -i Final-dvf-vs-viral_95.fasta -e 1e-5 -d home/databases/vironomy/vironomy_database//vironomy_database -p 20 Loading reference matrix Traceback (most recent call last): File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 207, in <module> main() File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 204, in main cli() File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1130, in __call__ return self.main(*args, **kwargs) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/home/choaro/.local/lib/python3.9/site-packages/click/decorators.py", line 26, in new_func return f(get_current_context(), *args, **kwargs) File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 191, in end_to_end markermatrix,distances = ctx.invoke(classify,inputs = inputs,hmmdb = hmmdb, multicopy = multicopy,force = force,taxonomiclevel=taxonomiclevel,dbdir = dbdir,outputdir = outputdir,hitstoreport = hitstoreport,subcluster = subcluster,evaluecutoff = evaluecutoff,threads = threads,tmpdir = tmpdir) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 65, in classify data = queryset(hmmdb=hmmdb,fastafile = inputs,taxonomiclevel=taxonomiclevel,multicopy = multicopystatus,hitstoreport = hitstoreport,subcluster = subcluster,fulldb = fulldb,markermatrixref = markermatrixref,taxmapping = taxmap,hmmpath = hmmpath,threads = threads,evaluecutoff = evaluecutoff,tmpdir = tmpdir,outputdir = outputdir) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/vironomy/classify.py", line 21, in __init__ self.referencedbs, self.taxmap = import_reference_dbs(markermatrixref,taxmapping) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/vironomy/utils.py", line 17, in import_reference_dbs markers = pd.read_csv(markermatrixref,index_col=0) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 575, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 934, in __init__ self._engine = self._make_engine(f, self.engine) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1218, in _make_engine self.handles = get_handle( # type: ignore[call-overload] File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/common.py", line 786, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: 'home/databases/vironomy/vironomy_database//vironomy_database/Genus_single_copy_marker_database.csv'

Can you please assist?

b-tierney commented 1 year ago

Ah I recently changed the database, pushed some code, but haven’t fixed the remote db version. Will update and inform you when it’s done.

On May 17, 2023, at 9:07 AM, Choaro @.***> wrote:

I successfully installed vironomy and downloaded the database.

Here is the database list:

-rw-r--r--. 1 choaro choaro 2210577317 Sep 8 2022 full_sc_marker_db.csv -rw-r--r--. 1 choaro choaro 211679588 Sep 8 2022 genbank_pfam_tgirfam_all_annotations_sc.txt -rw-r--r--. 1 choaro choaro 808969139 Sep 8 2022 genbank_predicted_proteins.faa -rw-r--r--. 1 choaro choaro 6673835 Sep 8 2022 group_taxid_contigid_mapping_annotation_data.tsv -rw-r--r--. 1 choaro choaro 1117845224 Sep 8 2022 single_copy_marker_database.csv -rw-r--r--. 1 choaro choaro 2203529712 Sep 8 2022 single_copy_marker_db.hmm

I have one fasta file with alll the viral contigs from virsorter2

when I run:

vironomy end_to_end -i Final-dvf-vs-viral_95.fasta -e 1e-5 -d home/databases/vironomy/vironomy_database//vironomy_database -p 20

I get this error message:

(vironomy) @. vironomy_database]$ vironomy end_to_end -i Final-dvf-vs-viral_95.fasta -e 1e-5 -d home/databases/vironomy/vironomy_database//vironomy_database -p 20 Loading reference matrix Traceback (most recent call last): File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 207, in main() File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 204, in main cli() File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1130, in call return self.main(args, kwargs) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(*args, *kwargs) File "/home/choaro/.local/lib/python3.9/site-packages/click/decorators.py", line 26, in new_func return f(get_current_context(), args, kwargs) File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 191, in end_to_end markermatrix,distances = ctx.invoke(classify,inputs = inputs,hmmdb = hmmdb, multicopy = multicopy,force = force,taxonomiclevel=taxonomiclevel,dbdir = dbdir,outputdir = outputdir,hitstoreport = hitstoreport,subcluster = subcluster,evaluecutoff = evaluecutoff,threads = threads,tmpdir = tmpdir) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 760, in invoke return callback(*args, **kwargs) File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 65, in classify data = queryset(hmmdb=hmmdb,fastafile = inputs,taxonomiclevel=taxonomiclevel,multicopy = multicopystatus,hitstoreport = hitstoreport,subcluster = subcluster,fulldb = fulldb,markermatrixref = markermatrixref,taxmapping = taxmap,hmmpath = hmmpath,threads = threads,evaluecutoff = evaluecutoff,tmpdir = tmpdir,outputdir = outputdir) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/vironomy/classify.py", line 21, in init self.referencedbs, self.taxmap = import_reference_dbs(markermatrixref,taxmapping) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/vironomy/utils.py", line 17, in import_reference_dbs markers = pd.read_csv(markermatrixref,index_col=0) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, kwargs) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 575, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 934, in init__ self._engine = self._make_engine(f, self.engine) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1218, in _make_engine self.handles = get_handle( # type: ignore[call-overload] File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/common.py", line 786, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: 'home/databases/vironomy/vironomy_database//vironomy_database/Genus_single_copy_marker_database.csv'

Can you please assist?

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b-tierney commented 1 year ago

Give it a try now?

Choaro commented 1 year ago

I tried downloaded the database and I got this error:

(vironomy) [choaro@marvin vironomy]$ vironomy download_db -p /home/databases/vironomy/ Downloading and untarring databases... --2023-05-18 14:02:12-- https://s3.us-east-1.wasabisys.com/vironomy-databases/vironomy_database.tar.gz Resolving s3.us-east-1.wasabisys.com (s3.us-east-1.wasabisys.com)... 38.27.106.30, 38.27.106.22, 38.27.106.107, ... Connecting to s3.us-east-1.wasabisys.com (s3.us-east-1.wasabisys.com)|38.27.106.30|:443... connected. GnuTLS: Error in the pull function. Unable to establish SSL connection. tar (child): /home/databases/vironomy//vironomy_database.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now Databases have been downloaded and unpacked. When you run vironomy, write your dbdir path as: /home/databases/vironomy//vironomy_database

Then I rerun the vironomy and i got the same error:

(vironomy) [choaro@marvin viral_host]$ vironomy end_to_end -i Final-dvf-vs-viral_95.fasta -e 1e-5 -d home/databases/vironomy/vironomy_database//vironomy_database -p 20 Loading reference matrix Traceback (most recent call last): File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 207, in <module> main() File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 204, in main cli() File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1130, in __call__ return self.main(*args, **kwargs) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/home/choaro/.local/lib/python3.9/site-packages/click/decorators.py", line 26, in new_func return f(get_current_context(), *args, **kwargs) File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 191, in end_to_end markermatrix,distances = ctx.invoke(classify,inputs = inputs,hmmdb = hmmdb, multicopy = multicopy,force = force,taxonomiclevel=taxonomiclevel,dbdir = dbdir,outputdir = outputdir,hitstoreport = hitstoreport,subcluster = subcluster,evaluecutoff = evaluecutoff,threads = threads,tmpdir = tmpdir) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 65, in classify data = queryset(hmmdb=hmmdb,fastafile = inputs,taxonomiclevel=taxonomiclevel,multicopy = multicopystatus,hitstoreport = hitstoreport,subcluster = subcluster,fulldb = fulldb,markermatrixref = markermatrixref,taxmapping = taxmap,hmmpath = hmmpath,threads = threads,evaluecutoff = evaluecutoff,tmpdir = tmpdir,outputdir = outputdir) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/vironomy/classify.py", line 21, in __init__ self.referencedbs, self.taxmap = import_reference_dbs(markermatrixref,taxmapping) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/vironomy/utils.py", line 17, in import_reference_dbs markers = pd.read_csv(markermatrixref,index_col=0) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 575, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 934, in __init__ self._engine = self._make_engine(f, self.engine) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1218, in _make_engine self.handles = get_handle( # type: ignore[call-overload] File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/common.py", line 786, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: 'home/databases/vironomy/vironomy_database//vironomy_database/Genus_single_copy_marker_database.csv'

b-tierney commented 1 year ago

Try downloading again? Seems like it was a permissions issue with the new update.

Choaro commented 1 year ago

Still getting the same error: `(vironomy) [choaro@marvin vironomy]$ vironomy download_db -p ./ Downloading and untarring databases... --2023-07-06 10:12:09-- https://s3.us-east-1.wasabisys.com/vironomy-databases/vironomy_database.tar.gz Resolving s3.us-east-1.wasabisys.com (s3.us-east-1.wasabisys.com)... 38.27.106.15, 38.27.106.107, 38.27.106.102, ... Connecting to s3.us-east-1.wasabisys.com (s3.us-east-1.wasabisys.com)|38.27.106.15|:443... connected. GnuTLS: Error in the pull function. Unable to establish SSL connection. tar (child): .//vironomy_database.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now Databases have been downloaded and unpacked. When you run vironomy, write your dbdir path as:

.//vironomy_database`

Loading reference matrix Traceback (most recent call last): File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 207, in <module> main() File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 204, in main cli() File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1130, in __call__ return self.main(*args, **kwargs) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/choaro/.local/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "/home/choaro/.conda/envs/mamba/envs/vironomy/bin/vironomy", line 65, in classify data = queryset(hmmdb=hmmdb,fastafile = inputs,taxonomiclevel=taxonomiclevel,multicopy = multicopystatus,hitstoreport = hitstoreport,subcluster = subcluster,fulldb = fulldb,markermatrixref = markermatrixref,taxmapping = taxmap,hmmpath = hmmpath,threads = threads,evaluecutoff = evaluecutoff,tmpdir = tmpdir,outputdir = outputdir) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/vironomy/classify.py", line 21, in __init__ self.referencedbs, self.taxmap = import_reference_dbs(markermatrixref,taxmapping) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/vironomy/utils.py", line 17, in import_reference_dbs markers = pd.read_csv(markermatrixref,index_col=0) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 575, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 934, in __init__ self._engine = self._make_engine(f, self.engine) File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1218, in _make_engine self.handles = get_handle( # type: ignore[call-overload] File "/home/choaro/.conda/envs/mamba/envs/vironomy/lib/python3.9/site-packages/pandas/io/common.py", line 786, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: '/home/databases/vironomy//Genus_single_copy_marker_database.csv'