strelka2 variants error

[sebastiandeorowicz]

NA12878 reads (coverage approx. 42x) mapped using bwa-0.7.15. Variant calling using Strelka2 2.9.9. Then, hap.py 0.3.10 fails with message:

[W] overlapping records at chr1:37070742 for sample 0 [W] Variants that overlap on the reference allele: 93 [I] Total VCF records: 3619471 [I] Non-reference VCF records: 3619471 [W] overlapping records at chr1:2121968 for sample 2 [W] Variants that overlap on the reference allele: 1741 [I] Total VCF records: 9071591 [I] Non-reference VCF records: 9066613 2018-10-04 15:55:48,393 ERROR Preprocess command preprocess /tmp/tmpb0jWSz.vcf.gz:* -l chr1:12963002-72309984 -o /tmp/input.chr1:12963002-72309984O6Vkph.prep.vcf.gz -V 1 -L 1 -r ../ref/hg38.fasta failed. Outputs are here /tmp/stdout38xEnE.log / /tmp/stderrv0vhIR.log 2018-10-04 15:55:48,393 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion !fmt->p_free' failed. 2018-10-04 15:55:48,393 ERROR Aborted 2018-10-04 15:55:48,393 ERROR Exception when running <function preprocessWrapper at 0x7fc6dd62cb90>: 2018-10-04 15:55:48,394 ERROR ------------------------------------------------------------ 2018-10-04 15:55:48,394 ERROR Traceback (most recent call last): 2018-10-04 15:55:48,394 ERROR File "/mnt/data01/mapper/apps/hap.py-0.3.10/lib/python27/Tools/parallel.py", line 72, in parMapper 2018-10-04 15:55:48,394 ERROR return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs']) 2018-10-04 15:55:48,394 ERROR File "/mnt/data01/mapper/apps/hap.py-0.3.10/lib/python27/Haplo/partialcredit.py", line 67, in preprocessWrapper 2018-10-04 15:55:48,394 ERROR subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe) 2018-10-04 15:55:48,395 ERROR File "/home/ODM/sdeorowicz/miniconda2/lib/python2.7/subprocess.py", line 190, in check_call 2018-10-04 15:55:48,395 ERROR raise CalledProcessError(retcode, cmd) 2018-10-04 15:55:48,395 ERROR CalledProcessError: Command 'preprocess /tmp/tmpb0jWSz.vcf.gz:* -l chr1:12963002-72309984 -o /tmp/input.chr1:12963002-72309984O6Vkph.prep.vcf.gz -V 1 -L 1 -r ../ref/hg38.fasta' returned non-zero exit status 134 2018-10-04 15:55:48,395 ERROR ------------------------------------------------------------ 2018-10-04 15:55:48,415 ERROR Preprocess command preprocess /tmp/tmpb0jWSz.vcf.gz:* -l chr12:9490309-34729213 -o /tmp/input.chr12:9490309-34729213lWGWKR.prep.vcf.gz -V 1 -L 1 -r ../ref/hg38.fasta failed. Outputs are here /tmp/stdoutzmxaVN.log / /tmp/stderrCnwHdq.log 2018-10-04 15:55:48,415 ERROR preprocess: vcf.c:3472: bcf_update_format: Assertion !fmt->p_free' failed. 2018-10-04 15:55:48,416 ERROR Aborted 2018-10-04 15:55:48,416 ERROR Exception when running <function preprocessWrapper at 0x7fc6dd62cb90>: 2018-10-04 15:55:48,416 ERROR ------------------------------------------------------------ 2018-10-04 15:55:48,416 ERROR Traceback (most recent call last): ...