FileNotFoundError: [Errno 2] No such file or directory: 'output.vcf.gz' [2025-07-08 13:12:09,890] - HAPPE - ERROR - convert file format. -- retrun code:256

[smrathod23]

HAPPE -g config.ini -v test.vcf.gz -i sample_inf.tsv -c sample.color -o output
[2025-07-08 13:12:09,818] - HAPPE - INFO - deal args.
[2025-07-08 13:12:09,819] - HAPPE - INFO - Filter samples and variants.
[2025-07-08 13:12:09,823] - HAPPE - INFO - convert file format.
Traceback (most recent call last):
File "/home/sachin215/miniconda3/envs/happe/lib/python3.13/site-packages/HAPPE/vcf2heatmatrix.py", line 30, in
inf = gzip.open(args.vcf,"rt") if args.vcf.endswith(".gz") else open(args.vcf,"r")
~~~~~~~~~^^^^^^^^^^^^^^^
File "/home/sachin215/miniconda3/envs/happe/lib/python3.13/gzip.py", line 66, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/home/sachin215/miniconda3/envs/happe/lib/python3.13/gzip.py", line 203, in init
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'output.vcf.gz'
[2025-07-08 13:12:09,890] - HAPPE - ERROR - convert file format. -- retrun code:256

I am getting this error again and again though after following the instruction. Please help me out to solve it.

[fengcong3]

Quick solution: Please use the -r parameter to specify the genomic interval or use the -s parameter to specify the SNP list. I will find time to fix this bug, thank you for your feedback.

[smrathod23]

Thank you for quick response, solution you provided has worked for me. but in output xlsx file I am not getting the haplotype frequency please give suggestion.