-
Notifications
You must be signed in to change notification settings - Fork 2
Description
Hello,
While running SeCNV, I get the following error:
$ python SeCNV.py /staging/leuven/stg_00096/home/dkresa/data/single_cell/230623.NovaSeq2.FCA/Snakemake/bam ./output /lustre1/project/stg_00096/references/GRCh38.alt-masked-V2/index/bwa-mem2/Homo_sapiens_assembly38_masked.fasta -r hg38 -p .bam
Constructing genome-wide consecutive bins...
Traceback (most recent call last):
File "/vsc-hard-mounts/leuven-data/343/vsc34319/miniconda3/envs/thesis/bin/faidx", line 10, in
sys.exit(main())
File "/vsc-hard-mounts/leuven-data/343/vsc34319/miniconda3/envs/thesis/lib/python3.9/site-packages/pyfaidx/cli.py", line 202, in main
write_sequence(args)
File "/vsc-hard-mounts/leuven-data/343/vsc34319/miniconda3/envs/thesis/lib/python3.9/site-packages/pyfaidx/cli.py", line 51, in write_sequence
outfile.write(transform_sequence(args, fasta, name, start, end))
File "/vsc-hard-mounts/leuven-data/343/vsc34319/miniconda3/envs/thesis/lib/python3.9/site-packages/pyfaidx/cli.py", line 121, in transform_sequence
line_len = fasta.faidx.index[name].lenc
KeyError: 'HLA-A01'
Calculating GC content...
Calculating mappability...
processing chromosomes......................
Calculating coverage...
File "/lustre1/project/stg_00096/home/dkresa/data/single_cell/230623.NovaSeq2.FCA/SeCNV/SeCNV/Scripts/call_cn.py", line 44
return matrix, chr_name, bin_list, sample_list
TabError: inconsistent use of tabs and spaces in indentation
Finish. Cost time 5630.809865474701 s
The files that have been already generated:
I tried with my reference genome but also the one you provided. The error is the same.
Do you know how to fix it?
Thanks!