Hello,
I have tried to reproduce the results of scANANSE manuscript using exemplary data. However, I got stuck on the final step that should predict the repressive TFs. I ran the pipeline in python following the code indicated in “AnanseScanpy_equivalent.pdf”.
On this line:
asc.import_scanpy_maelstrom(anndata=adata, cluster_id="predicted.id", maelstrom_dir="AnanseScanpy_outs/maelstrom/")
I received an error message
FileNotFoundError: [Errno 2] No such file or directory: 'AnanseScanpy_outs/maelstrom/final.out.txt
When I checked the generated files, the maelstrom folder and pfmscorefile.tsv file weren’t generated in previous steps of AnanseScanpy and anansnake. I understand that this line imports the motif enrichment results into the Scanpy object, but in my case this result is stored in another folder /AnanseScanpy_outs/gimme/pfmscorefile.tsv, which looks like
I therefore manually created a maelstrom folder and put the file pfmscorefile.tsv in there. I then changed the function import_scanpy_maelstrom() on line 187 in “anansescanpy_import.py” script as follows:
# Import the output df from maelstrom
# maelstrom_df = pd.read_csv(str(maelstrom_dir + "final.out.txt"),sep="\t",index_col=0)
maelstrom_df = pd.read_csv(str(maelstrom_dir + "pfmscorefile.tsv"),sep=",",index_col=0)
But I received another error from another function per_cluster_df()
ValueError: Length mismatch: Expected axis has 0 elements, new values have 131368 elements
Thus, I wanted to ask: what is this “AnanseScanpy_outs/maelstrom/final.out.txt” file? Should I exclude first 4 rows of pfmscorefile.tsv and save it as final.out.txt? The anansnake step didn't give me error messages.
Please find attached log file:
2024-09-23T143049.814049.snakemake.log
I ran scANANSE on a high-performance computing cluster provided within university, instead of my local PC. Could that be a reason why?
Your help would be greatly appreciated!
Best,
Xinqi
Hello,
I have tried to reproduce the results of scANANSE manuscript using exemplary data. However, I got stuck on the final step that should predict the repressive TFs. I ran the pipeline in python following the code indicated in “AnanseScanpy_equivalent.pdf”.
On this line:
asc.import_scanpy_maelstrom(anndata=adata, cluster_id="predicted.id", maelstrom_dir="AnanseScanpy_outs/maelstrom/")I received an error message
FileNotFoundError: [Errno 2] No such file or directory: 'AnanseScanpy_outs/maelstrom/final.out.txt
When I checked the generated files, the maelstrom folder and pfmscorefile.tsv file weren’t generated in previous steps of AnanseScanpy and anansnake. I understand that this line imports the motif enrichment results into the Scanpy object, but in my case this result is stored in another folder /AnanseScanpy_outs/gimme/pfmscorefile.tsv, which looks like
I therefore manually created a maelstrom folder and put the file pfmscorefile.tsv in there. I then changed the function import_scanpy_maelstrom() on line 187 in “anansescanpy_import.py” script as follows:
But I received another error from another function per_cluster_df()
ValueError: Length mismatch: Expected axis has 0 elements, new values have 131368 elements
Thus, I wanted to ask: what is this “AnanseScanpy_outs/maelstrom/final.out.txt” file? Should I exclude first 4 rows of pfmscorefile.tsv and save it as final.out.txt? The anansnake step didn't give me error messages.
Please find attached log file:
2024-09-23T143049.814049.snakemake.log
I ran scANANSE on a high-performance computing cluster provided within university, instead of my local PC. Could that be a reason why?
Your help would be greatly appreciated!
Best,
Xinqi