pre.py -> vcfcheck fails due to call with invalid genotype (non-existent allele)

[robertzeibich]

When I run hap.py with an already reduced TRUTH_VCF and QUERY_VCF, I get the following error:

python /projects/xm41/tools/hap/hap.py-build/bin/hap.py joint.gatk.vqsr.pass.FORMATrm.chr12:20723743-20766328.vcf.gz joint.deepv.FORMATrm.chr12:20723743-2076
6328.vcf.gz -f /projects/xm41/robert/compDeepVGATK/HG001_GRCh38_1_22_v4.2.1_benchmark_HC.bed.gz -r /scratch/xm41/hg38_resources/resources_broad_hg38_v0_Homo_
sapiens_assembly38.fasta -o chr12.19061524-21472881.FORMATrm.GATKts_DEEPV
[I] Total VCF records:         379
[I] Non-reference VCF records: 379
[I] Total VCF records:         361
[I] Non-reference VCF records: 361
Hap.py v0.3.15
2022-12-02 11:09:54,706 WARNING  [W] too many AD fields at chr12:20740786 max_ad = 9 retrieved: 12
2022-12-02 11:09:54,706 WARNING  *** Error in `xcmp': free(): invalid next size (fast): 0x0000000001952db0 ***
2022-12-02 11:09:54,706 WARNING  ======= Backtrace: =========
2022-12-02 11:09:54,706 WARNING  /lib64/libc.so.6(+0x81329)[0x7f8107a0b329]
2022-12-02 11:09:54,706 WARNING  xcmp(_ZN7variant13VariantReader7advanceEv+0x20fe)[0x542e94]
2022-12-02 11:09:54,706 WARNING  xcmp(_ZN7variant13VariantReader7advanceEv+0x2aeb)[0x543881]
2022-12-02 11:09:54,706 WARNING  xcmp(main+0x26fd)[0x504d97]
2022-12-02 11:09:54,706 WARNING  /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f81079ac555]
2022-12-02 11:09:54,706 WARNING  xcmp[0x500df5]
2022-12-02 11:09:54,706 WARNING  ======= Memory map: ========
2022-12-02 11:09:54,706 WARNING  00400000-0071b000 r-xp 00000000 622:b8b9a 144115453793453417             /fs04/xm41/tools/hap/hap.py-build/bin/xcmp
2022-12-02 11:09:54,706 WARNING  0091b000-00922000 r--p 0031b000 622:b8b9a 144115453793453417             /fs04/xm41/tools/hap/hap.py-build/bin/xcmp
2022-12-02 11:09:54,706 WARNING  00922000-00923000 rw-p 00322000 622:b8b9a 144115453793453417             /fs04/xm41/tools/hap/hap.py-build/bin/xcmp
2022-12-02 11:09:54,706 WARNING  00923000-00938000 rw-p 00000000 00:00 0
2022-12-02 11:09:54,706 WARNING  01442000-01bc6000 rw-p 00000000 00:00 0                                  [heap]
2022-12-02 11:09:54,706 WARNING  7f8040000000-7f8040021000 rw-p 00000000 00:00 0
2022-12-02 11:09:54,707 WARNING  7f8040021000-7f8044000000 ---p 00000000 00:00 0
2022-12-02 11:09:54,707 WARNING  7f8045c18000-7f8045c2d000 r-xp 00000000 fd:00 33554540                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2022-12-02 11:09:54,707 WARNING  7f8045c2d000-7f8045e2c000 ---p 00015000 fd:00 33554540                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2022-12-02 11:09:54,707 WARNING  7f8045e2c000-7f8045e2d000 r--p 00014000 fd:00 33554540                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2022-12-02 11:09:54,707 WARNING  7f8045e2d000-7f8045e2e000 rw-p 00015000 fd:00 33554540                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2022-12-02 11:09:54,707 WARNING  7f8045e2e000-7f810798a000 r--p 00000000 a2:41038 144116334077174665      /fs03/xm41/hg38_resources/resources_broad_hg38_v0_H
omo_sapiens_assembly38.fasta
2022-12-02 11:09:54,707 WARNING  7f810798a000-7f8107b4e000 r-xp 00000000 fd:00 33558864                   /usr/lib64/libc-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8107b4e000-7f8107d4d000 ---p 001c4000 fd:00 33558864                   /usr/lib64/libc-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8107d4d000-7f8107d51000 r--p 001c3000 fd:00 33558864                   /usr/lib64/libc-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8107d51000-7f8107d53000 rw-p 001c7000 fd:00 33558864                   /usr/lib64/libc-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8107d53000-7f8107d58000 rw-p 00000000 00:00 0
2022-12-02 11:09:54,707 WARNING  7f8107d58000-7f8107e59000 r-xp 00000000 fd:00 33558874                   /usr/lib64/libm-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8107e59000-7f8108058000 ---p 00101000 fd:00 33558874                   /usr/lib64/libm-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8108058000-7f8108059000 r--p 00100000 fd:00 33558874                   /usr/lib64/libm-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8108059000-7f810805a000 rw-p 00101000 fd:00 33558874                   /usr/lib64/libm-2.17.so
2022-12-02 11:09:54,707 WARNING  7f810805a000-7f8108071000 r-xp 00000000 fd:00 33558898                   /usr/lib64/libpthread-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8108071000-7f8108270000 ---p 00017000 fd:00 33558898                   /usr/lib64/libpthread-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8108270000-7f8108271000 r--p 00016000 fd:00 33558898                   /usr/lib64/libpthread-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8108271000-7f8108272000 rw-p 00017000 fd:00 33558898                   /usr/lib64/libpthread-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8108272000-7f8108276000 rw-p 00000000 00:00 0
2022-12-02 11:09:54,707 WARNING  7f8108276000-7f8108298000 r-xp 00000000 fd:00 33558857                   /usr/lib64/ld-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8108315000-7f8108376000 rw-p 00000000 00:00 0
2022-12-02 11:09:54,707 WARNING  7f8108376000-7f81083d7000 rw-p 00000000 00:00 0
2022-12-02 11:09:54,707 WARNING  7f81083d7000-7f8108438000 rw-p 00000000 00:00 0
2022-12-02 11:09:54,707 WARNING  7f8108469000-7f810846d000 rw-p 00000000 00:00 0
2022-12-02 11:09:54,707 WARNING  7f8108474000-7f8108497000 rw-p 00000000 00:00 0
2022-12-02 11:09:54,707 WARNING  7f8108497000-7f8108498000 r--p 00021000 fd:00 33558857                   /usr/lib64/ld-2.17.so
2022-12-02 11:09:54,707 WARNING  7f8108498000-7f8108499000 rw-p 00022000 fd:00 33558857                   /usr/lib64/ld-2.17.so
2022-12-02 11:09:54,708 WARNING  7f8108499000-7f810849a000 rw-p 00000000 00:00 0
2022-12-02 11:09:54,708 WARNING  7ffe79461000-7ffe79483000 rw-p 00000000 00:00 0                          [stack]
2022-12-02 11:09:54,708 WARNING  7ffe7951b000-7ffe7951d000 r-xp 00000000 00:00 0                          [vdso]
2022-12-02 11:09:54,708 WARNING  ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
2022-12-02 11:09:54,708 ERROR    Exception when running <function xcmpWrapper at 0x7f9e6d427de8>:
2022-12-02 11:09:54,708 ERROR    ------------------------------------------------------------
2022-12-02 11:09:54,708 ERROR    Traceback (most recent call last):
2022-12-02 11:09:54,708 ERROR      File "/fs04/xm41/tools/hap/hap.py-build/lib/python27/Tools/parallel.py", line 71, in parMapper
2022-12-02 11:09:54,709 ERROR        return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2022-12-02 11:09:54,709 ERROR      File "/fs04/xm41/tools/hap/hap.py-build/lib/python27/Haplo/xcmp.py", line 69, in xcmpWrapper
2022-12-02 11:09:54,710 ERROR        subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2022-12-02 11:09:54,710 ERROR      File "/usr/local/python/2.7.12-gcc4/lib/python2.7/subprocess.py", line 541, in check_call
2022-12-02 11:09:54,711 ERROR        raise CalledProcessError(retcode, cmd)
2022-12-02 11:09:54,712 ERROR    CalledProcessError: Command 'xcmp /tmp/truth.ppmhVMhm.vcf.gz /tmp/query.ppb20Y3m.vcf.gz -l chr12:20734455-20746140 -o /tmp/r
esult.chr12:20734455-20746140qHl6Jg.bcf -r /scratch/xm41/hg38_resources/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -f 0 -n 16768 --expand-hapblock
s 30 --window 50 --no-hapcmp 0 --qq QUAL' returned non-zero exit status -6
2022-12-02 11:09:54,712 ERROR    ------------------------------------------------------------
2022-12-02 11:09:54,989 ERROR    One of the xcmp jobs failed.
2022-12-02 11:09:54,989 ERROR    Traceback (most recent call last):
2022-12-02 11:09:54,989 ERROR      File "/projects/xm41/tools/hap/hap.py-build/bin/hap.py", line 540, in <module>
2022-12-02 11:09:54,990 ERROR        main()
2022-12-02 11:09:54,990 ERROR      File "/projects/xm41/tools/hap/hap.py-build/bin/hap.py", line 463, in main
2022-12-02 11:09:54,990 ERROR        raise Exception("One of the xcmp jobs failed.")
2022-12-02 11:09:54,990 ERROR    Exception: One of the xcmp jobs failed.

I have already removed the information in the INFO and FORMAT except from the GT. Due to the error, I thought of pre.py. When I run pre.py, I receive a VCF that contains calls with invalid genotype[s] (non existent allele) at chr12:119344875.
Do I have to filter them out one by one in order to use hap.py?

Help would be much appreciated!