Error upgrading bcbio-nextgen to add the genome and an aligner

[moutazhelal]

Thank you very much for looking into my issue
I am having a problem installing bcbio-nextgen on my local system. My goal is to run somatic mutation analysis on a bulkRNA seq data

Version info

• bcbio version (1.2.9)
• OS name and version (AlmaLinux 9.3 (Shamrock Pampas Cat)

I used the following command to start the installation without any data

python3 bcbio_nextgen_install.py /bcbio --tooldir=/bcbio/tools --nodata

Then I tried to upgrade by adding a genome and aligner

bcbio_nextgen.py upgrade -u skip --genomes hg38 --aligners bwa

after running for some time it returned the following error

Writing to .7deX3z
[W::vcf_parse_info] Extreme INFO/RS value encountered and set to missing at NC_000001.11:6259533
[buf_flush] Error: cannot write to .7deX3z/00111.bcf
Cleaning
tbx_index_build failed: dbsnp-156.vcf.gz
Traceback (most recent call last):
File "/home/moutaz/Documents/bcbio/bcbio/tools/bin/bcbio_nextgen.py", line 228, in
install.upgrade_bcbio(kwargs["args"])
File "/home/moutaz/Documents/bcbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/install.py", line 109, in upgrade_bcbio
upgrade_bcbio_data(args, REMOTES)
File "/home/moutaz/Documents/bcbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/install.py", line 361, in upgrade_bcbio_data
args.cores, ["ggd", "s3", "raw"])
File "/home/moutaz/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 354, in install_data_local
_prep_genomes(env, genomes, genome_indexes, ready_approaches, data_filedir)
File "/home/moutaz/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 480, in _prep_genomes
retrieve_fn(env, manager, gid, idx)
File "/home/moutaz/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 875, in _install_with_ggd
ggd.install_recipe(os.getcwd(), env.system_install, recipe_file, gid)
File "/home/moutaz/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 30, in install_recipe
recipe["recipe"]["full"]["recipe_type"], system_install)
File "/home/moutaz/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 62, in _run_recipe
subprocess.check_output(["bash", run_file])
File "/home/moutaz/Documents/bcbio/bcbio/anaconda/lib/python3.7/subprocess.py", line 411, in check_output
**kwargs).stdout
File "/home/moutaz/Documents/bcbio/bcbio/anaconda/lib/python3.7/subprocess.py", line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['bash', '/home/moutaz/Documents/bcbio/bcbio/genomes/Hsapiens/hg38/txtmp/ggd-run.sh']' returned non-zero exit status 1.

I will appreciate any help,
Thanks in advance,
Moutaz