Hi there, I am running into an issue while trying to run hap.py using the scmp-distance engine. The relevant output is below:
2023-09-05 06:43:47,418 INFO bcftools index -f -t /tmp/query.ppYfi9iI.vcf.gz
2023-09-05 06:43:50,097 INFO preprocess for /tmp/query.ppYfi9iI.vcf.gz -- time taken 479.19
2023-09-05 06:43:50,098 INFO bcftools merge --force-samples /tmp/truth.pp5XHAG2.vcf.gz /tmp/query.ppYfi9iI.vcf.gz -o /tmp/tmp45liHG
2023-09-05 06:43:50,289 ERROR Exception when running scmp: Command line bcftools merge --force-samples /tmp/truth.pp5XHAG2.vcf.gz /tmp/query.ppYfi9iI.vcf.gz -o /tmp/tmp45liHG got return code 255.
STDOUT:
STDERR: Incorrect number of FORMAT/AD values at chr1:13613, cannot merge. The tag is defined as Number=A, but found
2 values and 2 alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields
2023-09-05 06:43:50,289 ERROR ------------------------------------------------------------
2023-09-05 06:43:50,289 ERROR Traceback (most recent call last):
2023-09-05 06:43:50,289 ERROR File "/home/ubuntu/.conda/envs/happy/lib/python27/Haplo/scmp.py", line 45, in runSCmp
2023-09-05 06:43:50,289 ERROR runBcftools(*vargs)
2023-09-05 06:43:50,289 ERROR File "/home/ubuntu/.conda/envs/happy/lib/python27/Tools/bcftools.py", line 64, in runBcftools
2023-09-05 06:43:50,289 ERROR return runShellCommand('bcftools', *args)
2023-09-05 06:43:50,290 ERROR File "/home/ubuntu/.conda/envs/happy/lib/python27/Tools/bcftools.py", line 52, in runShellCommand
2023-09-05 06:43:50,290 ERROR raise Exception("Command line {} got return code {}.\nSTDOUT: {}\nSTDERR: {}".format(cmd_line, return_code, stdout, stderr))
2023-09-05 06:43:50,290 ERROR Exception: Command line bcftools merge --force-samples /tmp/truth.pp5XHAG2.vcf.gz /tmp/query.ppYfi9iI.vcf.gz -o /tmp/tmp45liHG got return code 255.STDOUT: STDERR: Incorrect number of FORMAT/AD values at chr1:13613, cannot merge. The tag is defined as Number=A, but found2 values and 2 alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields
2023-09-05 06:43:50,290 ERROR ------------------------------------------------------------
2023-09-05 06:43:50,332 ERROR Command line bcftools merge --force-samples /tmp/truth.pp5XHAG2.vcf.gz /tmp/query.ppYfi9iI.vcf.gz -o /tmp/tmp45liHG got return code 255.
STDOUT:
STDERR: Incorrect number of FORMAT/AD values at chr1:13613, cannot merge. The tag is defined as Number=A, but found
2 values and 2 alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields
2023-09-05 06:43:50,332 ERROR Traceback (most recent call last):
2023-09-05 06:43:50,332 ERROR File "/home/ubuntu/.conda/envs/happy/bin/hap.py", line 540, in <module>
2023-09-05 06:43:50,332 ERROR main()
2023-09-05 06:43:50,332 ERROR File "/home/ubuntu/.conda/envs/happy/bin/hap.py", line 488, in main
2023-09-05 06:43:50,332 ERROR tempfiles += Haplo.scmp.runSCmp(args.vcf1, args.vcf2, output_name, args)
2023-09-05 06:43:50,332 ERROR File "/home/ubuntu/.conda/envs/happy/lib/python27/Haplo/scmp.py", line 45, in runSCmp
2023-09-05 06:43:50,332 ERROR runBcftools(*vargs)
2023-09-05 06:43:50,333 ERROR File "/home/ubuntu/.conda/envs/happy/lib/python27/Tools/bcftools.py", line 64, in runBcftools
2023-09-05 06:43:50,333 ERROR return runShellCommand('bcftools', *args)
2023-09-05 06:43:50,333 ERROR File "/home/ubuntu/.conda/envs/happy/lib/python27/Tools/bcftools.py", line 52, in runShellCommand
2023-09-05 06:43:50,333 ERROR raise Exception("Command line {} got return code {}.\nSTDOUT: {}\nSTDERR: {}".format(cmd_line, return_code, stdout, stderr))
2023-09-05 06:43:50,333 ERROR Exception: Command line bcftools merge --force-samples /tmp/truth.pp5XHAG2.vcf.gz /tmp/query.ppYfi9iI.vcf.gz -o /tmp/tmp45liHG got return code 255.STDOUT: STDERR: Incorrect number of FORMAT/AD values at chr1:13613, cannot merge. The tag is defined as Number=A, but found2 values and 2 alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields
I have tried removing the AD and GQ fields for both my input VCF and truth VCF. I have also tried both "Number=R" and "Number=." in the AD field. However none of those steps are working and it seems like its the intermediate files that need to be processed. Does anyone know any workarounds for this?
Hi there, I am running into an issue while trying to run hap.py using the scmp-distance engine. The relevant output is below:
I have tried removing the AD and GQ fields for both my input VCF and truth VCF. I have also tried both "Number=R" and "Number=." in the AD field. However none of those steps are working and it seems like its the intermediate files that need to be processed. Does anyone know any workarounds for this?