Error processing an INV
jjfarrell opened this issue · 6 comments
jjfarrell commented
This error below occurs when processing this INV called by MANTA. Any suggestions? The variant record is supplying a REF. ALT, SVLEN and an SVINSEQ.
chr6 2893187 MantaINV:4:20498:20498:4:0:0;MantaINV:61660:0:0:1:0:0 C <INV> 548 PASS END=2893191;SVTYPE=INV;SVLEN=4;CIPOS=0,4;CIEND=-4,0;HOMLEN=4;HOMSEQ=TATA;SVINSLEN=51;SVINSSEQ=ACGTATATATATACGTATATATAATATATATATTATATATACGTATATATA;INV5;AC=2;AN=9578;FIBC_P=-0.000417444;HWE_SLP_P=-0.195618;FIBC_I=-0.000417444;HWE_SLP_I=-0.195618;MAX_IF=0.749985;MIN_IF=0.749985;LLK0=-281075;BETA_IF=0.49997,-3.8073e-06,1.89345e-06,3.9655e-06,2.17351e-06;ANN=<INV>|intron_variant|MODIFIER|SERPINB9|ENSG00000170542|transcript|ENST00000380698.4|protein_coding|5/6|c.567+220_567+223inv||||||;NS=4789;AF=0.000208812;MAF=0.000208812;AC_Het=2;AC_Hom=0;AC_Hemi=0;HWE=1;ExcHet=0.999896
It would be nice to get the chromosome in the below error message when running when trouble shooting.
2020-03-09 10:26:55,417 ERROR Exception when running vcf2paragraph on /scratch/tmppmn0a0d6.vcf.gz
2020-03-09 10:26:55,421 ERROR Traceback (most recent call last):
2020-03-09 10:26:55,422 ERROR File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcf2paragraph/__init__.py", line 286, in run_vcf2paragraph alt_paths=params["alt_paths"])
2020-03-09 10:26:55,422 ERROR File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcf2paragraph/__init__.py", line 86, in convert_vcf ref, indexed_vcf.name, ins_info_key, chrom, start, end, ref_node_padding, allele_graph)
2020-03-09 10:26:55,422 ERROR File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcfgraph/vcfgraph.py", line 128, in create_from_vcf graph.add_record(record, allele_graph, varId, ins_info_key)
2020-03-09 10:26:55,422 ERROR File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcfgraph/vcfgraph.py", line 202, in add_record self.add_alt(vcf.pos, vcf.stop, ref_sequence, alt_sequence, alt_samples, refSamples)
2020-03-09 10:26:55,423 ERROR File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcfgraph/vcfgraph.py", line 296, in add_alt raise Exception("{}:{} missing REF or ALT sequence.".format(start, end))
2020-03-09 10:26:55,423 ERROR Exception: 2893187:2893191 missing REF or ALT sequence.
2020-03-09 10:26:55,506 ERROR VCF to JSON conversion failed.
2020-03-09 10:26:55,509 ERROR multiprocessing.pool.RemoteTraceback: """Traceback (most recent call last): File "/share/pkg.7/python3/3.6.9/install/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "/share/pkg.7/python3/3.6.9/install/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar return list(map(*args)) File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcf2paragraph/__init__.py", line 286, in run_vcf2paragraph alt_paths=params["alt_paths"]) File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcf2paragraph/__init__.py", line 86, in convert_vcf ref, indexed_vcf.name, ins_info_key, chrom, start, end, ref_node_padding, allele_graph) File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcfgraph/vcfgraph.py", line 128, in create_from_vcf graph.add_record(record, allele_graph, varId, ins_info_key) File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcfgraph/vcfgraph.py", line 202, in add_record self.add_alt(vcf.pos, vcf.stop, ref_sequence, alt_sequence, alt_samples, refSamples) File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcfgraph/vcfgraph.py", line 296, in add_alt raise Exception("{}:{} missing REF or ALT sequence.".format(start, end))Exception: 2893187:2893191 missing REF or ALT sequence."""
2020-03-09 10:26:55,509 ERROR The above exception was the direct cause of the following exception:
2020-03-09 10:26:55,510 ERROR Traceback (most recent call last):
2020-03-09 10:26:55,510 ERROR File "/share/pkg.7/paragraph/2.4a/install/bin/multigrmpy.py", line 52, in load_graph_description header, records, event_list = convert_vcf_to_json(args, alt_paths=True)
2020-03-09 10:26:55,510 ERROR File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcf2paragraph/__init__.py", line 156, in convert_vcf_to_json variants = pool.map(run_vcf2paragraph, zip(to_process, itertools.repeat(params)))
2020-03-09 10:26:55,510 ERROR File "/share/pkg.7/python3/3.6.9/install/lib/python3.6/multiprocessing/pool.py", line 266, in map return self._map_async(func, iterable, mapstar, chunksize).get()
2020-03-09 10:26:55,510 ERROR File "/share/pkg.7/python3/3.6.9/install/lib/python3.6/multiprocessing/pool.py", line 644, in get raise self._value
2020-03-09 10:26:55,511 ERROR Exception: 2893187:2893191 missing REF or ALT sequence.
2020-03-09 10:26:55,511 ERROR multiprocessing.pool.RemoteTraceback: """Traceback (most recent call last): File "/share/pkg.7/python3/3.6.9/install/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "/share/pkg.7/python3/3.6.9/install/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar return list(map(*args)) File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcf2paragraph/__init__.py", line 286, in run_vcf2paragraph alt_paths=params["alt_paths"]) File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcf2paragraph/__init__.py", line 86, in convert_vcf ref, indexed_vcf.name, ins_info_key, chrom, start, end, ref_node_padding, allele_graph) File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcfgraph/vcfgraph.py", line 128, in create_from_vcf graph.add_record(record, allele_graph, varId, ins_info_key) File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcfgraph/vcfgraph.py", line 202, in add_record self.add_alt(vcf.pos, vcf.stop, ref_sequence, alt_sequence, alt_samples, refSamples) File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcfgraph/vcfgraph.py", line 296, in add_alt raise Exception("{}:{} missing REF or ALT sequence.".format(start, end))Exception: 2893187:2893191 missing REF or ALT sequence."""
2020-03-09 10:26:55,511 ERROR The above exception was the direct cause of the following exception:
2020-03-09 10:26:55,511 ERROR Traceback (most recent call last):
2020-03-09 10:26:55,512 ERROR File "/share/pkg.7/paragraph/2.4a/install/bin/multigrmpy.py", line 261, in run graph_files = load_graph_description(args)
2020-03-09 10:26:55,512 ERROR File "/share/pkg.7/paragraph/2.4a/install/bin/multigrmpy.py", line 52, in load_graph_description header, records, event_list = convert_vcf_to_json(args, alt_paths=True)
2020-03-09 10:26:55,512 ERROR File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcf2paragraph/__init__.py", line 156, in convert_vcf_to_json variants = pool.map(run_vcf2paragraph, zip(to_process, itertools.repeat(params)))
2020-03-09 10:26:55,512 ERROR File "/share/pkg.7/python3/3.6.9/install/lib/python3.6/multiprocessing/pool.py", line 266, in map return self._map_async(func, iterable, mapstar, chunksize).get()
2020-03-09 10:26:55,512 ERROR File "/share/pkg.7/python3/3.6.9/install/lib/python3.6/multiprocessing/pool.py", line 644, in get raise self._value
2020-03-09 10:26:55,513 ERROR Exception: 2893187:2893191 missing REF or ALT sequence.
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/share/pkg.7/python3/3.6.9/install/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/share/pkg.7/python3/3.6.9/install/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcf2paragraph/__init__.py", line 286, in run_vcf2paragraph
alt_paths=params["alt_paths"])
File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcf2paragraph/__init__.py", line 86, in convert_vcf
ref, indexed_vcf.name, ins_info_key, chrom, start, end, ref_node_padding, allele_graph)
File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcfgraph/vcfgraph.py", line 128, in create_from_vcf
graph.add_record(record, allele_graph, varId, ins_info_key)
File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcfgraph/vcfgraph.py", line 202, in add_record
self.add_alt(vcf.pos, vcf.stop, ref_sequence, alt_sequence, alt_samples, refSamples)
File "/share/pkg.7/paragraph/2.4a/install/lib/python3/grm/vcfgraph/vcfgraph.py", line 296, in add_alt
raise Exception("{}:{} missing REF or ALT sequence.".format(start, end))
Exception: 2893187:2893191 missing REF or ALT sequence.
"""
traxexx commented
For , Paragraph inverts REF sequences as ALT. Here, the REF sequence is C (padding base) + ATAT. After reverse complement, ATAT is still ATAT. There is a trimming step in graph building phase that eliminates same bases between REF and ALT. In this variant, all bases will be trimmed because they're the same...That's why you see this error message.
Actually this representation is confusing. It is a but it also has a INS sequence. @ctsa , what is the supposed ALT of this variant?
Thanks for reporting! v2.5 release will have a better error message on this situation.
jjfarrell commented
There is also a dup occurring at that site which may be complicating things:
chr6 2893187 MantaDUP:TANDEM:1:7410:7410:0:0:0;MantaDUP:TANDEM:8:21094:21094:1:0:0;MantaDUP:TANDEM:129143:0:0:0:0:0;MantaDUP:TANDEM:6:14973:14973:1:0:0;MantaDUP:TANDEM:98545:0:0:1:0:0;MantaDUP:TANDEM:62990:0:0:0:0:0;MantaDUP:TANDEM:66816:0:0:0:0:0;MantaDUP:TANDEM:2:21984:21984:1:0:0;MantaDUP:TANDEM:80362:0:0:0:0:0;MantaDUP:TANDEM:98083:0:0:0:0:0;MantaDUP:TANDEM:0:14436:14436:1:0:0;MantaDUP:TANDEM:7:10192:10192:0:0:0;MantaDUP:TANDEM:64160:0:0:0:0:0;MantaDUP:TANDEM:1:7753:7753:1:0:0;MantaDUP:TANDEM:4:10949:10949:1:0:0;MantaDUP:TANDEM:7:18966:18966:1:0:0;MantaDUP:TANDEM:7:12669:12669:1:0:0;MantaDUP:TANDEM:92715:0:0:1:0:0;MantaDUP:TANDEM:4:20498:20498:2:0:0;MantaDUP:TANDEM:75085:0:0:0:0:0;MantaDUP:TANDEM:0:13648:13648:1:0:0;MantaDUP:TANDEM:4:27357:27357:2:0:0;MantaDUP:TANDEM:75213:0:0:1:0:0;MantaDUP:TANDEM:0:5270:5270:1:0:0;MantaDUP:TANDEM:1:19103:19103:0:0:0;MantaDUP:TANDEM:2:15517:15517:1:0:0;MantaDUP:TANDEM:9:21216:21216:1:0:0;MantaDUP:TANDEM:5:13582:13582:1:0:0;MantaDUP:TANDEM:10:22557:22557:1:0:0;MantaDUP:TANDEM:0:13311:13311:1:0:0;MantaDUP:TANDEM:5:17416:17416:1:0:0;MantaDUP:TANDEM:63471:0:0:0:0:0;MantaDUP:TANDEM:5:21672:21672:1:0:0;MantaDUP:TANDEM:72641:0:0:0:0:0;MantaDUP:TANDEM:98874:0:0:1:0:0;MantaDUP:TANDEM:6:657:657:1:0:0;MantaDUP:TANDEM:64844:0:0:1:0:0;MantaDUP:TANDEM:69361:0:0:1:0:0;MantaDUP:TANDEM:8:18459:18459:1:0:0;MantaDUP:TANDEM:72455:0:0:0:0:0;MantaDUP:TANDEM:0:15177:15177:0:0:0;MantaDUP:TANDEM:82543:0:0:3:0:0;MantaDUP:TANDEM:100101:0:0:1:0:0;MantaDUP:TANDEM:3:34491:34491:2:0:0;MantaDUP:TANDEM:5:453:453:1:0:0;MantaDUP:TANDEM:71920:0:0:0:0:0;MantaDUP:TANDEM:75375:0:0:1:0:0;MantaDUP:TANDEM:8:22540:22540:1:0:0;MantaDUP:TANDEM:64714:0:0:0:0:0;MantaDUP:TANDEM:7:22858:22858:1:0:0;MantaDUP:TANDEM:68345:0:0:1:0:0;MantaDUP:TANDEM:64591:0:0:1:0:0;MantaDUP:TANDEM:7:9560:9560:1:0:0;MantaDUP:TANDEM:7:13563:13563:1:0:0;MantaDUP:TANDEM:64147:0:0:0:0:0;MantaDUP:TANDEM:71934:0:0:1:0:0;MantaDUP:TANDEM:2:15250:15250:1:0:0;MantaDUP:TANDEM:99981:0:0:1:0:0;MantaDUP:TANDEM:9:17467:17467:1:0:0;MantaDUP:TANDEM:0:22764:22764:1:0:0;MantaDUP:TANDEM:62283:0:0:0:0:0;MantaDUP:TANDEM:63120:0:0:2:0:0;MantaDUP:TANDEM:71271:0:0:1:0:0;MantaDUP:TANDEM:67500:0:0:1:0:0;MantaDUP:TANDEM:2:16398:16398:2:0:0;MantaDUP:TANDEM:6:13162:13162:0:0:0;MantaDUP:TANDEM:1:14161:14161:1:0:0;MantaDUP:TANDEM:3:24085:24085:1:0:0;MantaDUP:TANDEM:7:12967:12967:1:0:0;MantaDUP:TANDEM:0:9569:9569:2:0:0;MantaDUP:TANDEM:0:14270:14270:0:0:0;MantaDUP:TANDEM:7:17630:17630:0:0:0;MantaDUP:TANDEM:6:18095:18095:1:0:0;MantaDUP:TANDEM:6:23905:23905:1:0:0;MantaDUP:TANDEM:0:22231:22231:1:0:0;MantaDUP:TANDEM:0:486:486:0:0:0;MantaDUP:TANDEM:8:14872:14872:1:0:0;MantaDUP:TANDEM:65293:0:0:0:0:0;MantaDUP:TANDEM:2:22295:22295:0:0:0;MantaDUP:TANDEM:58519:0:0:0:0:0;MantaDUP:TANDEM:72661:0:0:1:0:0;MantaDUP:TANDEM:3:10030:10030:0:0:0;MantaDUP:TANDEM:12:23318:23318:0:0:0;MantaDUP:TANDEM:68906:0:0:0:0:0;MantaDUP:TANDEM:2:23725:23725:1:0:0;MantaDUP:TANDEM:0:15831:15831:0:0:0;MantaDUP:TANDEM:0:14511:14511:1:0:0;MantaDUP:TANDEM:72897:0:0:0:0:0;MantaDUP:TANDEM:74685:0:0:1:0:0;MantaDUP:TANDEM:77171:0:0:0:0:0;MantaDUP:TANDEM:59940:0:0:1:0:0;MantaDUP:TANDEM:3:8655:8655:0:0:0;MantaDUP:TANDEM:121919:0:0:1:0:0;MantaDUP:TANDEM:3:25904:25904:1:0:0;MantaDUP:TANDEM:182664:0:0:0:0:0;MantaDUP:TANDEM:175535:0:0:1:0:0;MantaDUP:TANDEM:62179:0:0:0:0:0;MantaDUP:TANDEM:8:16507:16507:1:0:0;MantaDUP:TANDEM:72402:0:0:0:0:0;MantaDUP:TANDEM:2:23155:23155:1:0:0;MantaDUP:TANDEM:1:14600:14600:1:0:0;MantaDUP:TANDEM:83098:0:0:2:0:0;MantaDUP:TANDEM:9:14467:14467:1:0:0;MantaDUP:TANDEM:80811:0:0:1:1:0;MantaDUP:TANDEM:86188:0:0:0:0:0;MantaDUP:TANDEM:10:22971:22971:0:0:0;MantaDUP:TANDEM:79300:0:0:1:0:0;MantaDUP:TANDEM:0:7401:7401:1:0:0;MantaDUP:TANDEM:45452:2:2:0:0:0;MantaDUP:TANDEM:3:15870:15870:1:0:0;MantaDUP:TANDEM:3:11374:11374:2:0:0;MantaDUP:TANDEM:72609:0:0:1:0:0;MantaDUP:TANDEM:137152:0:0:1:0:0;MantaDUP:TANDEM:0:9487:9487:1:0:0;MantaDUP:TANDEM:82080:0:0:2:0:0;MantaDUP:TANDEM:7:9696:9696:1:0:0;MantaDUP:TANDEM:3:14348:14348:1:0:0;MantaDUP:TANDEM:9:20435:20435:2:0:0;MantaDUP:TANDEM:2:24123:24123:1:0:0;MantaDUP:TANDEM:3:22140:22140:1:0:0;MantaDUP:TANDEM:0:16235:16235:1:0:0;MantaDUP:TANDEM:4:14045:14045:1:0:0;MantaDUP:TANDEM:10:15659:15659:1:0:0;MantaDUP:TANDEM:1:18638:18638:1:0:0;MantaDUP:TANDEM:3:16875:16875:1:0:0;MantaDUP:TANDEM:4:25043:25043:0:0:0;MantaDUP:TANDEM:0:9348:9348:1:0:0;MantaDUP:TANDEM:4:17754:17754:1:0:0;MantaDUP:TANDEM:70281:0:0:0:0:0;MantaDUP:TANDEM:163067:0:0:1:0:0;MantaDUP:TANDEM:100520:0:0:1:0:0;MantaDUP:TANDEM:70090:0:0:1:0:0;MantaDUP:TANDEM:159967:0:0:0:0:0;MantaDUP:TANDEM:5:12184:12184:0:0:0;MantaDUP:TANDEM:75650:0:0:1:0:0;MantaDUP:TANDEM:2:23861:23861:1:0:0;MantaDUP:TANDEM:69456:0:0:2:0:0;MantaDUP:TANDEM:23549:0:0:1:1:0;MantaDUP:TANDEM:68231:0:0:0:0:0;MantaDUP:TANDEM:72959:0:0:1:0:0;MantaDUP:TANDEM:72122:0:0:0:0:0;MantaDUP:TANDEM:61304:0:0:1:0:0;MantaDUP:TANDEM:55396:0:0:1:0:0;MantaDUP:TANDEM:57607:0:0:0:0:0;MantaDUP:TANDEM:15:23890:23890:2:0:0;MantaDUP:TANDEM:65646:0:0:1:0:0;MantaDUP:TANDEM:73940:0:0: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C <DUP:TANDEM> 999 PASS END=2893231;SVTYPE=DUP;SVLEN=44;SVINSLEN=73;SVINSSEQ=ATTATATATACGTATATATATACGTATATATAATATATATATTATATATACGTATATATAATATATATATATT;AC=217;AN=9578;FIBC_P=-0.0433043;HWE_SLP_P=-42.1212;FIBC_I=-0.0433133;HWE_SLP_I=-42.1553;MAX_IF=0.759877;MIN_IF=0.748001;LLK0=-268836;BETA_IF=0.505578,0.0461633,0.0721978,0.0701312,0.0841303;ANN=<DUP:TANDEM>|intron_variant|MODIFIER|SERPINB9|ENSG00000170542|transcript|ENST00000380698.4|protein_coding|5/6|c.567+180_567+223dup||||||;NS=4789;AF=0.0226561;MAF=0.0226561;AC_Het=211;AC_Hom=6;AC_Hemi=0;HWE=0.736495;ExcHet=0.771593
chr6 2893187 MantaINV:4:20498:20498:4:0:0;MantaINV:61660:0:0:1:0:0 C <INV> 548 PASS END=2893191;SVTYPE=INV;SVLEN=4;CIPOS=0,4;CIEND=-4,0;HOMLEN=4;HOMSEQ=TATA;SVINSLEN=51;SVINSSEQ=ACGTATATATATACGTATATATAATATATATATTATATATACGTATATATA;INV5;AC=2;AN=9578;FIBC_P=-0.000417444;HWE_SLP_P=-0.195618;FIBC_I=-0.000417444;HWE_SLP_I=-0.195618;MAX_IF=0.749985;MIN_IF=0.749985;LLK0=-281075;BETA_IF=0.49997,-3.8073e-06,1.89345e-06,3.9655e-06,2.17351e-06;ANN=<INV>|intron_variant|MODIFIER|SERPINB9|ENSG00000170542|transcript|ENST00000380698.4|protein_coding|5/6|c.567+220_567+223inv||||||;NS=4789;AF=0.000208812;MAF=0.000208812;AC_Het=2;AC_Hom=0;AC_Hemi=0;HWE=1;ExcHet=0.999896
traxexx commented
Let me try to check with Chris internally. For now I recommend skipping such ambiguous records.
KamilSJaron commented
I got the same problem with the following entry
scaf000253 514459 MantaINV:5899:0:0:0:0:0 N <INV> 34 SampleFT END=514542;SVTYPE=INV;SVLEN=83;IMPRECISE;CIPOS=-351,352;CIEND=-355,356;INV5 GT:FT:GQ:PL:PR 1/1:MinGQ:9:86,12,0:0,4
That same problem: Exception: 514459:514542 missing REF or ALT sequence.
Funny enough, this is for sure a wrong call or misassembly because it's the same individual that was used to build the reference.
If I would understand better on what paragraph expect, I could ad appropriate adjustments in the following script to get them the manta output to paragraph compatible vcf file
traxexx commented
Your error is exactly the same as above. For now I suggest not including such records before figuring out what Manta really means for them.
KamilSJaron commented
As discussed in the last post of #42, SVINSSEQ is part of variants that are breakpoints with insertions. I.e. nested variants; inversions with an insertion on aside.
My solution was to filter them out.