Unknown issue

[thesamuanels]

Hello,
I've been trying to run ViralRecall, both using the test provided and with my own data, but it always gives me the following error:

Traceback (most recent call last):
File "/opt/viralrecall/viralrecall.py", line 733, in <module>
status = main()
File "/opt/viralrecall/viralrecall.py", line 725, in main
run_program(newinput, newproject, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel)
File "/opt/viralrecall/viralrecall.py", line 475, in run_program
summary = summary.append(data)
File "/opt/Anaconda3/envs/viralrecall/lib/python3.10/site-packages/pandas/core/generic.py", line 5989, in __getattr__
return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'?

Any idea what the issue might be?

[faylward]

What was your command and input? I found that many errors can be fixed by playing around with the python version. Frank

…

On Mon, Jan 29, 2024, 8:22 PM DGian ***@***.***> wrote: Hello, I've been trying to run ViralRecall, both using the test provided and with my own data, but it always gives me the following error: Traceback (most recent call last): File "/opt/viralrecall/viralrecall.py", line 733, in <module> status = main() File "/opt/viralrecall/viralrecall.py", line 725, in main run_program(newinput, newproject, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel) File "/opt/viralrecall/viralrecall.py", line 475, in run_program summary = summary.append(data) File "/opt/Anaconda3/envs/viralrecall/lib/python3.10/site-packages/pandas/core/generic.py", line 5989, in __getattr__ return object.__getattribute__(self, name) AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'? Any idea what the issue might be? — Reply to this email directly, view it on GitHub <#24>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACPFN7WVGG6BRRXXZ4FD7VDYRBDLVAVCNFSM6AAAAABCQMVGPOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGEYDMNZWG44DAMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[thesamuanels]

The input for that specific output was:
python /opt/viralrecall/viralrecall.py -i test -c -p viralrecall.out -b -e 1e-5
However, I got the same error when running:
python viralrecall.py -i examples/arm29B.fna -p test_outdir -t 2 -f

I have downgraded to python 3.5.6, now when running
python /opt/viralrecall/viralrecall.py -i test -c -p viralrecall.out -b -e 1e-5

I've obtained:

Running viralrecall on ALA.Apr2023.130_S8_metabat2.7.fa and output will be deposited in viralrecall.out/ALA.Apr2023.130_S8_metabat2.7.fa
Traceback (most recent call last):
File "/opt/viralrecall/viralrecall.py", line 733, in <module>
status = main()
File "/opt/viralrecall/viralrecall.py", line 725, in main
run_program(newinput, newproject, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel)
File "/opt/viralrecall/viralrecall.py", line 401, in run_program
df = pandas.concat([df, s1], axis=1, sort=True)
TypeError: concat() got an unexpected keyword argument 'sort'

[faylward]

Yeah I think this is an issue with the Pandas version then. They changed the way that data frames can be sorted. So maybe downgrade the pandas version? Sorry I can't be more specific. Frank

…

On Tue, Jan 30, 2024, 5:02 PM DGian ***@***.***> wrote: The input for that specific output was: python /opt/viralrecall/viralrecall.py -i test -c -p viralrecall.out -b -e 1e-5 However, I got the same error when running: python viralrecall.py -i examples/arm29B.fna -p test_outdir -t 2 -f I have downgraded to python 3.5.6, now when running python /opt/viralrecall/viralrecall.py -i test -c -p viralrecall.out -b -e 1e-5 I've obtained: Running viralrecall on ALA.Apr2023.130_S8_metabat2.7.fa and output will be deposited in viralrecall.out/ALA.Apr2023.130_S8_metabat2.7.fa Traceback (most recent call last): File "/opt/viralrecall/viralrecall.py", line 733, in status = main() File "/opt/viralrecall/viralrecall.py", line 725, in main run_program(newinput, newproject, database, window, phagesize, minscore, minhit, evalue, cpus, plotflag, redo, flanking, batch, summary_file, contiglevel) File "/opt/viralrecall/viralrecall.py", line 401, in run_program df = pandas.concat([df, s1], axis=1, sort=True) TypeError: concat() got an unexpected keyword argument 'sort'` And when running — Reply to this email directly, view it on GitHub <#24 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACPFN7RSI4TT3YIUQXTU7RTYRFUWVAVCNFSM6AAAAABCQMVGPOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJXHE3DSNJTGE> . You are receiving this because you commented.Message ID: ***@***.***>

[thesamuanels]

Solved! Thanks.
We actually had an older version of pandas in our conda environment. It works now with pandas 0.23.0

[faylward]

Great! Glad it worked out. Frank

…

On Tue, Jan 30, 2024, 7:20 PM DGian ***@***.***> wrote: Solved! Thanks. We actually had an older version of pandas in our conda environment. It works now with pandas 0.23.0 — Reply to this email directly, view it on GitHub <#24 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACPFN7SFTBV7DZ252IGRWDDYRGE6JAVCNFSM6AAAAABCQMVGPOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJYGEZTOMZZGY> . You are receiving this because you commented.Message ID: ***@***.***>