init_genome error

[lingchuanmeixi]

When I enter "wgbtools init_home - f hg38", I get“[wt init] Setting up genome reference files in ./software/wgbs_tools/references/hg38 [wt init] No reference FASTA provided. Attempting to download from https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 938M 100 938M 0 0 6153k 0 0:02:36 0:02:36 --:--:-- 3578k [wt init] successfully downloaded FASTA. Now gunzip and bgzip it... bgzip: invalid option -- '@' [bgzip] No such file or directory: 12 Traceback (most recent call last):File "./software/wgbs_tools/wgbstools", line 96, in main() File "./software/wgbs_tools/wgbstools", line 63, in main importlib.import_module(args.command).main() File "./software/wgbs_tools/src/python/init_genome.py", line 297, in main InitGenome(args).run() File "./software/wgbs_tools/src/python/init_genome.py", line 57, in init self.get_fasta() File "./software/wgbs_tools/src/python/init_genome.py", line 79, in get_fasta subprocess.check_call(cmd, shell=True) File "./miniconda3/miniconda3/lib/python3.9/subprocess.py", line 373, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'gunzip ./wgbs_tools/references/hg38/hg38.fa.gz && bgzip -@ 12 ./wgbs_tools/references/hg38/hg38.fa' returned non-zero exit status 1.”

My configuration： python3 ，pandas version1.5.1，numpy version1.23.4， scipy version1.9.3 htslib version1.13

[lingchuanmeixi]

I removed the -@ part of init_genome.py. Although the reason for the error is not clear, the program can run normally.

[gibberwocky]

This error is due to using an out-of-date version of htslib. The -@ flag specifies the number of threads to use (http://www.htslib.org/doc/bgzip.html). Updating to htslib 1.18 will solve this.

[lingchuanmeixi]

您好，您的邮件已收到，会尽快回复！

[Guoyixian1989]

Thank you very much