Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

While using hap.py, there is a problem: #189

Open
pioneer-pi opened this issue Jul 13, 2024 · 0 comments
Open

While using hap.py, there is a problem: #189

pioneer-pi opened this issue Jul 13, 2024 · 0 comments

Comments

@pioneer-pi
Copy link

I use docker to start hap.py.
The docker sentences:

docker run -it \
  -v "${PWD}":"/input" \
  -v "${PWD}/my_output:/output" \
  jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \
  /input/chr20.vcf.gz \
  /output/my.vcf \
  -f "/input/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_chr.bed" \
  -r "/input/ucsc_hg19.fa" \
  -o "/output/happy.output" \
  --engine=vcfeval \
  --pass-only \
  -l chr20

The error information is :

2024-07-13 12:29:32,677 WARNING  Creating template for vcfeval. You can speed this up by supplying a SDF template that corresponds to /input/ucsc_hg19.fa
2024-07-13 12:30:43,939 ERROR    Error running rtg tools / vcfeval. Return code was 1, output:  / null
Error: RTG has encountered a difficulty, please contact [email protected]
Please send the log file ('/tmp/vcfeval.result3BAEs0.dir/vcfeval.log') to Real Time Genomics at [email protected]
 

2024-07-13 12:30:43,939 ERROR    Traceback (most recent call last):
2024-07-13 12:30:43,939 ERROR      File "/opt/hap.py/bin/hap.py", line 529, in <module>
2024-07-13 12:30:43,939 ERROR        main()
2024-07-13 12:30:43,939 ERROR      File "/opt/hap.py/bin/hap.py", line 473, in main
2024-07-13 12:30:43,939 ERROR        tempfiles += Haplo.vcfeval.runVCFEval(args.vcf1, args.vcf2, output_name, args)
2024-07-13 12:30:43,939 ERROR      File "/opt/hap.py/lib/python27/Haplo/vcfeval.py", line 132, in runVCFEval
2024-07-13 12:30:43,940 ERROR        raise Exception("Error running rtg tools / vcfeval. Return code was %i, output: %s / %s \n" % (rc, o, e))
2024-07-13 12:30:43,940 ERROR    Exception: Error running rtg tools / vcfeval. Return code was 1, output:  / nullError: RTG has encountered a difficulty, please contact [email protected] send the log file ('/tmp/vcfeval.result3BAEs0.dir/vcfeval.log') to Real Time Genomics at [email protected]
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant