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clb21565 / mobileOG-db

code repo for mobileOG-db
GNU General Public License v3.0
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Output error #6

Closed kayanac closed 1 year ago

kayanac commented 1 year ago

Hello!

I am getting the error below after I run ./mobileOGs-pl-kyanite.sh -i NFEBO18_contigs_1000.fasta -d mobileOG-db-beatrix-1.6.dmnd -m mobileOG-db-beatrix-1.6.All.csv -k 15 -e 1e-20 -p 90 -q 90 > sample.txt. Can you help me with solving this issue?

Error mesage:

Error: Invalid output field: qtitle Traceback (most recent call last): File "/Users/yanack/kadir/Databases/mobileOG-db/mobileOGs-pl-kyanite.py", line 19, in df_OUT=pd.read_csv(args.i,sep="\t") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/util/_decorators.py", line 211, in wrapper return func(*args, *kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/util/_decorators.py", line 331, in wrapper return func(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv return _read(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 605, in _read parser = TextFileReader(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1442, in init self._engine = self._make_engine(f, self.engine) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1735, in _make_engine self.handles = get_handle( ^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/io/common.py", line 856, in get_handle handle = open( ^^^^^ FileNotFoundError: [Errno 2] No such file or directory: 'NFEBO18_contigs_1000.fasta.tsv'

Thanks,

clb21565 commented 1 year ago

Hey there, thanks for using our tool!

I think the issue is that you are piping the command to > sample.txt. Is there a specific reason for this? You should be able to run the pipeline without it.

My guess is that the intermediate output (...)fasta.tsv is not being generated because of this.

./mobileOGs-pl-kyanite.sh -i NFEBO18_contigs_1000.fasta -d mobileOG-db-beatrix-1.6.dmnd -m mobileOG-db-beatrix-1.6.All.csv -k 15 -e 1e-20 -p 90 -q 90

should work

kayanac commented 1 year ago

Hello, thank you for your quick reply.

I got the same error when I run your command (without piping the command to > sample.txt). It does not generate the .tsv file. Please see the error below.

"Error: Invalid output field: qtitle Traceback (most recent call last): File "/Users/yanack/kadir/Databases/mobileOG-db/mobileOGs-pl-kyanite.py", line 19, in df_OUT=pd.read_csv(args.i,sep="\t") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/util/_decorators.py", line 211, in wrapper return func(*args, *kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/util/_decorators.py", line 331, in wrapper return func(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv return _read(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 605, in _read parser = TextFileReader(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1442, in init self._engine = self._make_engine(f, self.engine) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1735, in _make_engine self.handles = get_handle( ^^^^^^^^^^^ File "/Users/yanack/anaconda3/envs/mamba/envs/mobileOG-db/lib/python3.11/site-packages/pandas/io/common.py", line 856, in get_handle handle = open( ^^^^^ FileNotFoundError: [Errno 2] No such file or directory: 'NFEBO18_contigs_1000.fasta.tsv'

clb21565 commented 1 year ago

Weird!

Do you have a .faa file from prodigal? if yes,

Can you see any diamond output? if no,

is it possible your contigs have no MGE hallmark genes?

Also I notice your python version looks to be 3.11 based on the path. Could you confirm this doing python -v ?

I wonder if updating it to 3.6.15 would fix it?

kayanac commented 1 year ago

Hello,

I have a file from prodigal but I dont see any diamond output. I know there must be MGE hallmark genes in my sample.

Yes, I am using a different version of python. When I tried to create mobileOG-db environment with conda create -n mobileOG-db python=3.6.15, I got the error below and I could not fix it.

'Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

clb21565 commented 1 year ago

The python version might also be an error, but it wouldn't explain the missing diamond output. Can you confirm that diamond is installed? What happens when you try to blastp the .faa file against the diamond database?

I am not sure what to suggest regarding the python version issue. It may or may not error out when running the python script, but, the issue with env. solving sounds like a conda environment issue on your end

Sorry about that!

At the end of the day, all we are really doing here is querying the orfs against the database and summarizing the results. It should be relatively easy to reproduce the script by running diamond yourself and importing the results into a jupyter notebook, or running the python script in a different environment with the correct version. Let me know if you are able to solve it.

On Tue, Dec 27, 2022 at 3:43 PM kayanac @.***> wrote:

Hello,

I have a file from prodigal but I dont see any diamond output. I know there must be MGE hallmark genes in my sample.

Yes, I am using a different version of python. When I tried to create mobileOG-db environment with conda create -n mobileOG-db python=3.6.15, I got the error below and I could not fix it.

'Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  • python=3.6.15

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

— Reply to this email directly, view it on GitHub https://github.com/clb21565/mobileOG-db/issues/6#issuecomment-1366171665, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIM35ZH3TABU2O5OZA6XBHTWPNIIHANCNFSM6AAAAAATKEJS2I . You are receiving this because you commented.Message ID: @.***>

-- Connor Brown Graduate Research Assistant with Helm Lab https://www.biochem.vt.edu/people/faculty/helm-richard.html and Pruden Lab https://www.pruden.cee.vt.edu/ Department of Genetics, Bioinformatics, and Computational Biology Virginia Tech

kayanac commented 1 year ago

Hello,

I was able to install mobileOG-db with python=3.6.15 by removing some channels from conda. Now it is working fine.

Thanks

clb21565 commented 1 year ago

great!