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Unknown issue #24
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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?
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The input for that specific output was: I have downgraded to python 3.5.6, now when running I've obtained:
|
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
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Solved! Thanks. |
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
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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?
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