Get something error in running the example.

[MartinChiaHsinLiu]

Hi, I install the hap.py through anaconda. When I run the test run: $ hap.py example/happy/PG_NA12878_chr21.vcf.gz example/happy/NA12878_chr21.vcf.gz -r example/chr21.fa -f example/happy/PG_Conf_chr21.bed.gz -o test

I get something error. May someone help me? Thank you a million.

2021-08-08 20:27:09,450 WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file. 2021-08-08 20:27:09,450 WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file. [W] overlapping records at chr21:10993857 for sample 0 [W] Symbolic / SV ALT alleles at chr21:15847469 [W] Variants that overlap on the reference allele: 144 [W] Variants that have symbolic ALT alleles: 14 [I] Total VCF records: 65402 [I] Non-reference VCF records: 65402 [W] overlapping records at chr21:24024261 for sample 0 [W] Variants that overlap on the reference allele: 5 [I] Total VCF records: 101524 [I] Non-reference VCF records: 101524 2021-08-08 20:27:40,250 ERROR [stderr] regex_error 2021-08-08 20:27:40,257 ERROR Command 'quantify /tmp/hap.py.result.mkd_6q.vcf.gz -o test.roc.tsv -r example/chr21.fa --threads 16 --output-vtc 0 --output-rocs 1 --type xcmp --qq IQQ --qq-header QUAL --roc-delta 0.500000 --clean-info 1 --fix-chr-regions 0 -v test.vcf.gz -R 'CONF_VARS:/tmp/tmp9lwgPm.bed' -R 'CONF:example/happy/PG_Conf_chr21.bed.gz' --roc-regions ''' returned non-zero exit status 1 2021-08-08 20:27:40,258 ERROR Traceback (most recent call last): 2021-08-08 20:27:40,258 ERROR File "/home/user/.conda/envs/happy/bin/hap.py", line 511, in 2021-08-08 20:27:40,259 ERROR main() 2021-08-08 20:27:40,259 ERROR File "/home/user/.conda/envs/happy/bin/hap.py", line 496, in main 2021-08-08 20:27:40,259 ERROR qfy.quantify(args) 2021-08-08 20:27:40,259 ERROR File "/home/user/.conda/envs/happy/bin/qfy.py", line 129, in quantify 2021-08-08 20:27:40,259 ERROR strat_fixchr=args.strat_fixchr) 2021-08-08 20:27:40,259 ERROR File "/home/user/.conda/envs/happy/lib/python27/Haplo/quantify.py", line 177, in run_quantify 2021-08-08 20:27:40,260 ERROR subprocess.check_call(run_str, shell=True, stdout=tfo, stderr=tfe) 2021-08-08 20:27:40,260 ERROR File "/home/user/.conda/envs/happy/lib/python2.7/subprocess.py", line 190, in check_call 2021-08-08 20:27:40,261 ERROR raise CalledProcessError(retcode, cmd) 2021-08-08 20:27:40,261 ERROR CalledProcessError: Command 'quantify /tmp/hap.py.result.mkd_6q.vcf.gz -o test.roc.tsv -r example/chr21.fa --threads 16 --output-vtc 0 --output-rocs 1 --type xcmp --qq IQQ --qq-header QUAL --roc-delta 0.500000 --clean-info 1 --fix-chr-regions 0 -v test.vcf.gz -R 'CONF_VARS:/tmp/tmp9lwgPm.bed' -R 'CONF:example/happy/PG_Conf_chr21.bed.gz' --roc-regions ''' returned non-zero exit status 1