Failure at Step 7/3 "Filtering blast data"

[psampara]

Hi Simon,
At the step 7/3 - “Link matching genomes to representatives and filter out redundant / useless matches... Filtering blast data”, the tool is failing.

The traceback I received is:
Traceback (most recent call last):
File "/project/st-ziels-1/minicoESC[CESC[CESC[C/envs/iphop_env/bin/iphop", line 10, in <module>
sys.exit(cli())
File "/project/st-ziels-1/minicoESC[CESC[CESC[C/envs/iphop_env/lib/python3.8/site-packages/iphop/iphop.py", line 128, in cli
args"func"
File "/project/st-ziels-1/minicoESC[CESC[CESC[C/envs/iphop_env/lib/python3.8/site-packages/iphop/modules/master_predict.py", line 102, in main
dataprep.aggregate(args)
File "/project/st-ziels-1/minicoESC[CESC[CESC[C/envs/iphop_env/lib/python3.8/site-packages/iphop/modules/dataprep.py", line 40, in aggregate
store_filtered = filter_hits(args,store,store_filtered,host_info)
File "/project/st-ziels-1/minicoESC[CESC[CESC[C/envs/iphop_env/lib/python3.8/site-packages/iphop/modules/dataprep.py", line 215, in filter_hits
store_filtered = store_filtered.append(df) ## Append should work directly now that we have matched all column and names nicely
File "/home/psampara/.local/lib/python3.8/site-packages/pandas/core/generic.py", line 5989, in getattr
return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'append'

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The full error is attached.

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The code I used is
iphop predict --fa_file $viral_contigs --db_dir $iphop_db/ --out_dir $iphop_out/ -t 32 --debug

I used 32 threads and 256 GB of memory

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Thanks!

Pranav

[Simon Roux]

HI Pranav,

This looks like an issue with the Pandas version (“append” was removed in the latest version of pandas). Can you check that your conda environment (as I think you installed iPHoP through conda) has the correct version of pandas ?

[psampara]

Thanks Simon! After moving to the correct version, I could run through the tool successfully.

[Simon Roux]

Perfect, glad that it worked in the end !

[Simon Roux]

Solved