Closed ramashka328 closed 11 months ago
When I try to add regional BED file from bed_files_of_interest (UCSC.k100_umap.without.repeatmasker.bed), I get a different error:
Traceback (most recent call last):
File "/data/projects/scrna_seq_active/SComatic/scripts/BaseCellCounter/BaseCellCounter.py", line 410, in <module>
main()
File "/data/projects/scrna_seq_active/SComatic/scripts/BaseCellCounter/BaseCellCounter.py", line 385, in main
BED = MakeWindows(CONTIG, FASTA, bed, bed_out, BIN)
File "/data/projects/scrna_seq_active/SComatic/scripts/BaseCellCounter/BaseCellCounter.py", line 108, in MakeWindows
inFasta.close()
UnboundLocalError: local variable 'inFasta' referenced before assignment
Python packages installed:
about-time 3.1.1 Jinja2 3.1.2 MarkupSafe 2.1.3 numpy 1.21.6 numpy-groupies 0.9.14 pandas 1.3.5 pip 23.2.1 pybedtools 0.8.1 pysam 0.16.0.1 python-dateutil 2.8.2 pytz 2023.3 rpy2 2.9.4 scipy 1.7.3 setuptools 47.1.0 six 1.16.0
Maybe you can replace the reference sequence with a special version for 10X.
Dear user,
Thanks for bringing this up. It should be fixed now. Do a git pull
of the tool and try again. Let me know if the error still persists.
Cheers, Fran
Hello,
thank you for your amazing work! I am trying to run SComatic scripts using singularity container with all requirements installed. The SplitBamCellTypes.py worked just fine and created separate BAM files for each cell type. However, when I try to run the BaseCellCounter.py script I get the following output:
I am running the following script:
What do you think could be the problem?