【need help】An error occurred when running to Merge

[SolarQuiltc]

Hi Brentp,I am very grateful for using your work，and an error occurred while I was running this step

smoove merge --name merged -f $reference_fasta --outdir ./ results-smoove/*.genotyped.vcf.gz

I ran the program in the format provided by README.md ,But the program exited smoove merge --name merged --fasta ./ARS-UCD1.2_Btau5.0.1Y.fa --outdir outdir/ ./*genotyped.vcf.gz

[smoove] 2023/07/13 18:57:24 starting with version 0.2.8 [smoove] 2023/07/13 18:57:24 merging 3 files [smoove] 2023/07/13 18:57:24 finished sorting 3 files; merge starting. 2023/07/13 18:57:24 exit status 1

Generated a file named “merged.lsort.vcf” , The content is as follows:

Traceback (most recent call last): File "/home/miniconda3/envs/smoove/bin/lsort", line 70, in sys.exit(main()) File "/home/miniconda3/envs/smoove/bin/lsort", line 27, in main samples = l_bp.parse_vcf(vcf_file_name, vcf_lines, vcf_headers) File "/home/miniconda3/envs/smoove/bin/l_bp.py", line 16, in parse_vcf f = open(vcf_file_name, 'r') IOError: [Errno 2] No such file or directory: '-r'

I tried to modify “l_bp.py” script did not solve the problem

Is it possible that the format of the command I entered was incorrect, which caused me to be unable to read the file correctly？

[zhachengwan]

Have you solved it? I have encountered the same problem. Could you please provide some help? Thank you.

[SolarQuiltc]

Have you solved it? I have encountered the same problem. Could you please provide some help? Thank you. Yes, I solved this problem. I wrote the new version of svtools into the current environment and then ran through this program