having troubles running dbCAN on WSL machine

[wasbornhere2019]

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while running dbCAN on WSL machine I get an error after using command
Name:~$ run_dbcan EscheriaColiK12MG1655.fna protein

1. DIAMOND start**********************

1. DIAMOND end************************

2. HMMER start**********************

Error: Sequence file output/uniInput is empty or misformatted

2. HMMER end************************

cat: output/h.out: No such file or directory

3. dbCAN_sub start************************

Error: Sequence file output/uniInput is empty or misformatted

total time: 0.0022652149200439453

3. dbCAN_sub end************************

File not found: output/dbcan-sub.hmm.out
File not found: [Errno 2] No such file or directory: 'output/hmmer.out'
Traceback (most recent call last):
File "/home/askar/miniconda3/bin/run_dbcan", line 10, in
sys.exit(cli_main())
^^^^^^^^^^
File "/home/askar/miniconda3/lib/python3.12/site-packages/dbcan/cli/run_dbcan.py", line 1098, in cli_main
run_dbCAN(
File "/home/askar/miniconda3/lib/python3.12/site-packages/dbcan/cli/run_dbcan.py", line 484, in run_dbCAN
with open(outDir + prefix + "diamond.out") as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'output/diamond.out'

How do I make it work and how does it usually run? how do i run dbCAN3 on my machine?

I'm sorry for those kinds of questions, I am new to this kind of workflow and I would like to learn

Thank you!

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[Xinpeng021001]

Hi, seems like the run_dbCAN does not find your input file and then it gives the error as no input (uniprot is the generated input file by the first step).

[wasbornhere2019]

Thank you so much for the quick reply! How do I fix this issue? Is there a specific way to do it or where should I look to find a solution to this problem? Thank you, Askar Takhirov

…

On Tue, Nov 12, 2024, 7:34 AM Xinpeng Zhang ***@***.***> wrote: Hi, seems like the run_dbCAN does not find your input file and then it gives the error as no input (uniprot is the generated input file by the first step). — Reply to this email directly, view it on GitHub <#190 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AXEXQHHPDSBV6OAQW5CWJJD2AINXPAVCNFSM6AAAAABRIESA7GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZQHA2TIMZWG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Xinpeng021001]

Thank you so much for the quick reply! How do I fix this issue? Is there a specific way to do it or where should I look to find a solution to this problem? Thank you, Askar Takhirov
…
On Tue, Nov 12, 2024, 7:34 AM Xinpeng Zhang @.> wrote: Hi, seems like the run_dbCAN does not find your input file and then it gives the error as no input (uniprot is the generated input file by the first step). — Reply to this email directly, view it on GitHub <#190 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AXEXQHHPDSBV6OAQW5CWJJD2AINXPAVCNFSM6AAAAABRIESA7GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZQHA2TIMZWG4 . You are receiving this because you authored the thread.Message ID: @.>

run_dbcan EscheriaColiK12MG1655.fna protein

I noticed that you used the "protein mode" for the run_dbCAN, however, your input file "EscheriaColiK12MG1655.fna" is the nucleotide sequence. You could use the "faa" file with "protein mode" or the "fna" file with "prok mode". You could also find it in our handbook.

[wasbornhere2019]

(base) askar@AskarLaptop:~$ run_dbcan EscheriaColiK12MG1655.faa protein

1. DIAMOND start**********************

1. DIAMOND end************************

2. HMMER start**********************

Error: Sequence file output/uniInput is empty or misformatted

2. HMMER end************************

cat: output/h.out: No such file or directory

3. dbCAN_sub start************************

Error: Sequence file output/uniInput is empty or misformatted

total time: 0.0022542476654052734

3. dbCAN_sub end************************

File not found: output/dbcan-sub.hmm.out
File not found: [Errno 2] No such file or directory: 'output/hmmer.out'
Traceback (most recent call last):
File "/home/askar/miniconda3/bin/run_dbcan", line 10, in
sys.exit(cli_main())
^^^^^^^^^^
File "/home/askar/miniconda3/lib/python3.12/site-packages/dbcan/cli/run_dbcan.py", line 1098, in cli_main
run_dbCAN(
File "/home/askar/miniconda3/lib/python3.12/site-packages/dbcan/cli/run_dbcan.py", line 484, in run_dbCAN
with open(outDir + prefix + "diamond.out") as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'output/diamond.out'

I am still getting the same error. Is there a way to make my computer see the input? Is this a common issue?

[Xinpeng021001]

you could use textmate or any text editor to open the input files and check if it works or not. Besides, seems like the diamond and hmmer dose not run successfully. I would suggest you test those by command lines.

[wasbornhere2019]

(base) askar@AskarLaptop:~$ run_dbcan EscheriaColiK12MG1655.fna prok

1. DIAMOND start**********************

1. DIAMOND end************************

2. HMMER start**********************

2. HMMER end************************

3. dbCAN_sub start************************

total time: 42.60253834724426

3. dbCAN_sub end************************

File not found: [Errno 2] No such file or directory: 'output/hmmer.out'
Preparing overview table from hmmer, dbCAN_sub and diamond output...
Overview table complete. Saved as output/overview.txt
(base) askar@AskarLaptop:~$ cat output/overview.txt
Gene ID EC# HMMER dbCAN_sub DIAMOND #ofTools

So I "fixed" the previous issue by downloading fna and faa files directly from github and now i cannot get the output, for faa file it fails and for fna it gives me an emty table.

PS. I really appreciate the help you are providing me with this project. I would love to talk to you about your system some time, from what I know this program is more than noteworthy and is a revelation that deserves both funding and further advancement