Comments (6)
rkimoakbioinformatics
commented on May 31, 2024
Hi, would it be possible for us to test with your input file? If not, can you inserting the following code at /data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/inout.py:155, so that the code looks like:
print(f'@ col_name={col_name} tok={tok} l={l}')
tok = json.loads(tok)
and let us know what you get in the output of the oc run?
from open-cravat.
mmterpstra
commented on May 31, 2024
Ok, just wait a minute or 200 or so.
from open-cravat.
mmterpstra
commented on May 31, 2024
The vanilla default log
2020/09/09 14:12:14 cravat.hgvs started: Wed Sep 9 14:12:14 2020
2020/09/09 14:12:33 cravat.mutation_assessor finished: Wed Sep 9 14:12:33 2020
2020/09/09 14:12:33 cravat.mutation_assessor runtime: 467.166s
2020/09/09 14:12:33 cravat.interpro started: Wed Sep 9 14:12:33 2020
2020/09/09 14:20:26 cravat.hgvs Traceback (most recent call last):
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/base_annotator.py", line 197, in run
output_dict = self.annotate(input_data)
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/modules/annotators/hgvs/hgvs.py", line 230, in annotate
hgvs_p = self._get_hgvs_p(tseq)
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/modules/annotators/hgvs/hgvs.py", line 180, in _get_hgvs_p
hit_aa = tseq.shared_phead[tseq.orig_ppos_start-1]
IndexError: string index out of range
2020/09/09 14:20:32 cravat.interpro finished: Wed Sep 9 14:20:32 2020
2020/09/09 14:20:32 cravat.interpro runtime: 478.781s
2020/09/09 14:24:44 cravat.gnomad finished: Wed Sep 9 14:24:44 2020
2020/09/09 14:24:44 cravat.gnomad runtime: 752.592s
2020/09/09 14:25:21 cravat.dbsnp finished: Wed Sep 9 14:25:21 2020
2020/09/09 14:25:21 cravat.dbsnp runtime: 889.141s
2020/09/09 14:32:03 cravat.hgvs Traceback (most recent call last):
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/base_annotator.py", line 197, in run
output_dict = self.annotate(input_data)
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/modules/annotators/hgvs/hgvs.py", line 230, in annotate
hgvs_p = self._get_hgvs_p(tseq)
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/modules/annotators/hgvs/hgvs.py", line 113, in _get_hgvs_p
hgvs_alt = '%sfs*%s' %(aa_let_to_abbv(tseq.palt_and_tail[0]), count_to_stop)
IndexError: string index out of range
2020/09/09 14:38:37 cravat.hgvs finished: Wed Sep 9 14:38:37 2020
2020/09/09 14:38:37 cravat.hgvs runtime: 1583.339s
2020/09/09 14:38:39 cravat.aggregator level: variant
2020/09/09 14:38:39 cravat.aggregator input directory: /path/tp/002/VariantAnnotation/oc
2020/09/09 14:54:49 cravat.aggregator started: Wed Sep 9 14:54:49 2020
2020/09/09 14:56:02 cravat An unexpected exception occurred.
Traceback (most recent call last):
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/cravat_class.py", line 382, in main
self.result_path = self.run_aggregator()
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/cravat_class.py", line 905, in run_aggregator
v_aggregator.run()
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/aggregator.py", line 141, in run
for lnum, line, rd in reader.loop_data():
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/inout.py", line 156, in loop_data
tok = json.loads(tok)
File "/software/software/Python/3.6.4-foss-2018a/lib/python3.6/json/__init__.py", line 354, in loads
return _default_decoder.decode(s)
File "/software/software/Python/3.6.4-foss-2018a/lib/python3.6/json/decoder.py", line 339, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/software/software/Python/3.6.4-foss-2018a/lib/python3.6/json/decoder.py", line 357, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
2020/09/09 14:56:02 cravat finished with an exception: Wed Sep 9 14:56:02 2020
2020/09/09 14:56:02 cravat runtime: 9178.057s
Last 50 lines of your requested (crude) dump (whole file 900K lines please do not ask me to copypaste that):
@ col_name=extra_vcf_info__RUN tok=1.0 l=9814 0.581395 0.405 5.48477 2.0 0.5 4.0 25.0 -0.076 1X 0.0 True 33.0 43.0 0.0 3.79203 4.9405 4.7712 1.377 0.581395 5.48477 2.0 0.5 4.0 25.0 1X 43.0 43.0 0.0 3.79203 4.9405 0.0 1.0 1.0 60.0 60.0 2.0 1.0 21.3277 1.0 0.888889 0.0 0.0 0.0 0.0 925.0 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 13.0 3.09716 12.0 11.0 4.9405 7.0 snp 1.0 56.44 80.5 26.16 0.0 2.0 0.5 4.0 -0.469 0.0 True 45.0 4.7712 1.217 2.0 0.5 60.0 0.0 12.1 -0.49 0.425 0.0 1.0 1.0 2.0 0.5 36.74 0.0 60.0 60.0 0.0 0.0 2.0 1.0 21.3277 0.0 1.0 0.888889 0.0 0.0 0.0 0.0 0.0 925.0 12.39 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 0.2 13.0 3.09716 12.0 4759 DOWNSTREAM NONE processed_transcript MROH7 MODIFIER ENST00000472987 0.596 11.0 4.9405 7.0 snp SNP COSV59872425 1.0 83.0 GATK-freebayes 1.0 A downstream_gene_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000472987.5 processed_transcript n.*4759G>A 4759
@ col_name=extra_vcf_info__ReadPosRankSum tok=0.2 l=9814 0.581395 0.405 5.48477 2.0 0.5 4.0 25.0 -0.076 1X 0.0 True 33.0 43.0 0.0 3.79203 4.9405 4.7712 1.377 0.581395 5.48477 2.0 0.5 4.0 25.0 1X 43.0 43.0 0.0 3.79203 4.9405 0.0 1.0 1.0 60.0 60.0 2.0 1.0 21.3277 1.0 0.888889 0.0 0.0 0.0 0.0 925.0 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 13.0 3.09716 12.0 11.0 4.9405 7.0 snp 1.0 56.44 80.5 26.16 0.0 2.0 0.5 4.0 -0.469 0.0 True 45.0 4.7712 1.217 2.0 0.5 60.0 0.0 12.1 -0.49 0.425 0.0 1.0 1.0 2.0 0.5 36.74 0.0 60.0 60.0 0.0 0.0 2.0 1.0 21.3277 0.0 1.0 0.888889 0.0 0.0 0.0 0.0 0.0 925.0 12.39 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 0.2 13.0 3.09716 12.0 4759 DOWNSTREAM NONE processed_transcript MROH7 MODIFIER ENST00000472987 0.596 11.0 4.9405 7.0 snp SNP COSV59872425 1.0 83.0 GATK-freebayes 1.0 A downstream_gene_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000472987.5 processed_transcript n.*4759G>A 4759
@ col_name=extra_vcf_info__SAF tok=13.0 l=9814 0.581395 0.405 5.48477 2.0 0.5 4.0 25.0 -0.076 1X 0.0 True 33.0 43.0 0.0 3.79203 4.9405 4.7712 1.377 0.581395 5.48477 2.0 0.5 4.0 25.0 1X 43.0 43.0 0.0 3.79203 4.9405 0.0 1.0 1.0 60.0 60.0 2.0 1.0 21.3277 1.0 0.888889 0.0 0.0 0.0 0.0 925.0 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 13.0 3.09716 12.0 11.0 4.9405 7.0 snp 1.0 56.44 80.5 26.16 0.0 2.0 0.5 4.0 -0.469 0.0 True 45.0 4.7712 1.217 2.0 0.5 60.0 0.0 12.1 -0.49 0.425 0.0 1.0 1.0 2.0 0.5 36.74 0.0 60.0 60.0 0.0 0.0 2.0 1.0 21.3277 0.0 1.0 0.888889 0.0 0.0 0.0 0.0 0.0 925.0 12.39 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 0.2 13.0 3.09716 12.0 4759 DOWNSTREAM NONE processed_transcript MROH7 MODIFIER ENST00000472987 0.596 11.0 4.9405 7.0 snp SNP COSV59872425 1.0 83.0 GATK-freebayes 1.0 A downstream_gene_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000472987.5 processed_transcript n.*4759G>A 4759
@ col_name=extra_vcf_info__SAP tok=3.09716 l=9814 0.581395 0.405 5.48477 2.0 0.5 4.0 25.0 -0.076 1X 0.0 True 33.0 43.0 0.0 3.79203 4.9405 4.7712 1.377 0.581395 5.48477 2.0 0.5 4.0 25.0 1X 43.0 43.0 0.0 3.79203 4.9405 0.0 1.0 1.0 60.0 60.0 2.0 1.0 21.3277 1.0 0.888889 0.0 0.0 0.0 0.0 925.0 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 13.0 3.09716 12.0 11.0 4.9405 7.0 snp 1.0 56.44 80.5 26.16 0.0 2.0 0.5 4.0 -0.469 0.0 True 45.0 4.7712 1.217 2.0 0.5 60.0 0.0 12.1 -0.49 0.425 0.0 1.0 1.0 2.0 0.5 36.74 0.0 60.0 60.0 0.0 0.0 2.0 1.0 21.3277 0.0 1.0 0.888889 0.0 0.0 0.0 0.0 0.0 925.0 12.39 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 0.2 13.0 3.09716 12.0 4759 DOWNSTREAM NONE processed_transcript MROH7 MODIFIER ENST00000472987 0.596 11.0 4.9405 7.0 snp SNP COSV59872425 1.0 83.0 GATK-freebayes 1.0 A downstream_gene_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000472987.5 processed_transcript n.*4759G>A 4759
@ col_name=extra_vcf_info__SAR tok=12.0 l=9814 0.581395 0.405 5.48477 2.0 0.5 4.0 25.0 -0.076 1X 0.0 True 33.0 43.0 0.0 3.79203 4.9405 4.7712 1.377 0.581395 5.48477 2.0 0.5 4.0 25.0 1X 43.0 43.0 0.0 3.79203 4.9405 0.0 1.0 1.0 60.0 60.0 2.0 1.0 21.3277 1.0 0.888889 0.0 0.0 0.0 0.0 925.0 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 13.0 3.09716 12.0 11.0 4.9405 7.0 snp 1.0 56.44 80.5 26.16 0.0 2.0 0.5 4.0 -0.469 0.0 True 45.0 4.7712 1.217 2.0 0.5 60.0 0.0 12.1 -0.49 0.425 0.0 1.0 1.0 2.0 0.5 36.74 0.0 60.0 60.0 0.0 0.0 2.0 1.0 21.3277 0.0 1.0 0.888889 0.0 0.0 0.0 0.0 0.0 925.0 12.39 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 0.2 13.0 3.09716 12.0 4759 DOWNSTREAM NONE processed_transcript MROH7 MODIFIER ENST00000472987 0.596 11.0 4.9405 7.0 snp SNP COSV59872425 1.0 83.0 GATK-freebayes 1.0 A downstream_gene_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000472987.5 processed_transcript n.*4759G>A 4759
@ col_name=extra_vcf_info__SOR tok=0.596 l=9814 0.581395 0.405 5.48477 2.0 0.5 4.0 25.0 -0.076 1X 0.0 True 33.0 43.0 0.0 3.79203 4.9405 4.7712 1.377 0.581395 5.48477 2.0 0.5 4.0 25.0 1X 43.0 43.0 0.0 3.79203 4.9405 0.0 1.0 1.0 60.0 60.0 2.0 1.0 21.3277 1.0 0.888889 0.0 0.0 0.0 0.0 925.0 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 13.0 3.09716 12.0 11.0 4.9405 7.0 snp 1.0 56.44 80.5 26.16 0.0 2.0 0.5 4.0 -0.469 0.0 True 45.0 4.7712 1.217 2.0 0.5 60.0 0.0 12.1 -0.49 0.425 0.0 1.0 1.0 2.0 0.5 36.74 0.0 60.0 60.0 0.0 0.0 2.0 1.0 21.3277 0.0 1.0 0.888889 0.0 0.0 0.0 0.0 0.0 925.0 12.39 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 0.2 13.0 3.09716 12.0 4759 DOWNSTREAM NONE processed_transcript MROH7 MODIFIER ENST00000472987 0.596 11.0 4.9405 7.0 snp SNP COSV59872425 1.0 83.0 GATK-freebayes 1.0 A downstream_gene_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000472987.5 processed_transcript n.*4759G>A 4759
@ col_name=extra_vcf_info__SRF tok=11.0 l=9814 0.581395 0.405 5.48477 2.0 0.5 4.0 25.0 -0.076 1X 0.0 True 33.0 43.0 0.0 3.79203 4.9405 4.7712 1.377 0.581395 5.48477 2.0 0.5 4.0 25.0 1X 43.0 43.0 0.0 3.79203 4.9405 0.0 1.0 1.0 60.0 60.0 2.0 1.0 21.3277 1.0 0.888889 0.0 0.0 0.0 0.0 925.0 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 13.0 3.09716 12.0 11.0 4.9405 7.0 snp 1.0 56.44 80.5 26.16 0.0 2.0 0.5 4.0 -0.469 0.0 True 45.0 4.7712 1.217 2.0 0.5 60.0 0.0 12.1 -0.49 0.425 0.0 1.0 1.0 2.0 0.5 36.74 0.0 60.0 60.0 0.0 0.0 2.0 1.0 21.3277 0.0 1.0 0.888889 0.0 0.0 0.0 0.0 0.0 925.0 12.39 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 0.2 13.0 3.09716 12.0 4759 DOWNSTREAM NONE processed_transcript MROH7 MODIFIER ENST00000472987 0.596 11.0 4.9405 7.0 snp SNP COSV59872425 1.0 83.0 GATK-freebayes 1.0 A downstream_gene_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000472987.5 processed_transcript n.*4759G>A 4759
@ col_name=extra_vcf_info__SRP tok=4.9405 l=9814 0.581395 0.405 5.48477 2.0 0.5 4.0 25.0 -0.076 1X 0.0 True 33.0 43.0 0.0 3.79203 4.9405 4.7712 1.377 0.581395 5.48477 2.0 0.5 4.0 25.0 1X 43.0 43.0 0.0 3.79203 4.9405 0.0 1.0 1.0 60.0 60.0 2.0 1.0 21.3277 1.0 0.888889 0.0 0.0 0.0 0.0 925.0 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 13.0 3.09716 12.0 11.0 4.9405 7.0 snp 1.0 56.44 80.5 26.16 0.0 2.0 0.5 4.0 -0.469 0.0 True 45.0 4.7712 1.217 2.0 0.5 60.0 0.0 12.1 -0.49 0.425 0.0 1.0 1.0 2.0 0.5 36.74 0.0 60.0 60.0 0.0 0.0 2.0 1.0 21.3277 0.0 1.0 0.888889 0.0 0.0 0.0 0.0 0.0 925.0 12.39 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 0.2 13.0 3.09716 12.0 4759 DOWNSTREAM NONE processed_transcript MROH7 MODIFIER ENST00000472987 0.596 11.0 4.9405 7.0 snp SNP COSV59872425 1.0 83.0 GATK-freebayes 1.0 A downstream_gene_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000472987.5 processed_transcript n.*4759G>A 4759
@ col_name=extra_vcf_info__SRR tok=7.0 l=9814 0.581395 0.405 5.48477 2.0 0.5 4.0 25.0 -0.076 1X 0.0 True 33.0 43.0 0.0 3.79203 4.9405 4.7712 1.377 0.581395 5.48477 2.0 0.5 4.0 25.0 1X 43.0 43.0 0.0 3.79203 4.9405 0.0 1.0 1.0 60.0 60.0 2.0 1.0 21.3277 1.0 0.888889 0.0 0.0 0.0 0.0 925.0 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 13.0 3.09716 12.0 11.0 4.9405 7.0 snp 1.0 56.44 80.5 26.16 0.0 2.0 0.5 4.0 -0.469 0.0 True 45.0 4.7712 1.217 2.0 0.5 60.0 0.0 12.1 -0.49 0.425 0.0 1.0 1.0 2.0 0.5 36.74 0.0 60.0 60.0 0.0 0.0 2.0 1.0 21.3277 0.0 1.0 0.888889 0.0 0.0 0.0 0.0 0.0 925.0 12.39 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 0.2 13.0 3.09716 12.0 4759 DOWNSTREAM NONE processed_transcript MROH7 MODIFIER ENST00000472987 0.596 11.0 4.9405 7.0 snp SNP COSV59872425 1.0 83.0 GATK-freebayes 1.0 A downstream_gene_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000472987.5 processed_transcript n.*4759G>A 4759
@ col_name=extra_vcf_info__dbSnpxCOMMON tok=1.0 l=9814 0.581395 0.405 5.48477 2.0 0.5 4.0 25.0 -0.076 1X 0.0 True 33.0 43.0 0.0 3.79203 4.9405 4.7712 1.377 0.581395 5.48477 2.0 0.5 4.0 25.0 1X 43.0 43.0 0.0 3.79203 4.9405 0.0 1.0 1.0 60.0 60.0 2.0 1.0 21.3277 1.0 0.888889 0.0 0.0 0.0 0.0 925.0 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 13.0 3.09716 12.0 11.0 4.9405 7.0 snp 1.0 56.44 80.5 26.16 0.0 2.0 0.5 4.0 -0.469 0.0 True 45.0 4.7712 1.217 2.0 0.5 60.0 0.0 12.1 -0.49 0.425 0.0 1.0 1.0 2.0 0.5 36.74 0.0 60.0 60.0 0.0 0.0 2.0 1.0 21.3277 0.0 1.0 0.888889 0.0 0.0 0.0 0.0 0.0 925.0 12.39 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 0.2 13.0 3.09716 12.0 4759 DOWNSTREAM NONE processed_transcript MROH7 MODIFIER ENST00000472987 0.596 11.0 4.9405 7.0 snp SNP COSV59872425 1.0 83.0 GATK-freebayes 1.0 A downstream_gene_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000472987.5 processed_transcript n.*4759G>A 4759
@ col_name=extra_vcf_info__dbSnpxdbSNPBuildID tok=83.0 l=9814 0.581395 0.405 5.48477 2.0 0.5 4.0 25.0 -0.076 1X 0.0 True 33.0 43.0 0.0 3.79203 4.9405 4.7712 1.377 0.581395 5.48477 2.0 0.5 4.0 25.0 1X 43.0 43.0 0.0 3.79203 4.9405 0.0 1.0 1.0 60.0 60.0 2.0 1.0 21.3277 1.0 0.888889 0.0 0.0 0.0 0.0 925.0 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 13.0 3.09716 12.0 11.0 4.9405 7.0 snp 1.0 56.44 80.5 26.16 0.0 2.0 0.5 4.0 -0.469 0.0 True 45.0 4.7712 1.217 2.0 0.5 60.0 0.0 12.1 -0.49 0.425 0.0 1.0 1.0 2.0 0.5 36.74 0.0 60.0 60.0 0.0 0.0 2.0 1.0 21.3277 0.0 1.0 0.888889 0.0 0.0 0.0 0.0 0.0 925.0 12.39 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 0.2 13.0 3.09716 12.0 4759 DOWNSTREAM NONE processed_transcript MROH7 MODIFIER ENST00000472987 0.596 11.0 4.9405 7.0 snp SNP COSV59872425 1.0 83.0 GATK-freebayes 1.0 A downstream_gene_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000472987.5 processed_transcript n.*4759G>A 4759
@ col_name=extra_vcf_info__technologyxillumina tok=1.0 l=9814 0.581395 0.405 5.48477 2.0 0.5 4.0 25.0 -0.076 1X 0.0 True 33.0 43.0 0.0 3.79203 4.9405 4.7712 1.377 0.581395 5.48477 2.0 0.5 4.0 25.0 1X 43.0 43.0 0.0 3.79203 4.9405 0.0 1.0 1.0 60.0 60.0 2.0 1.0 21.3277 1.0 0.888889 0.0 0.0 0.0 0.0 925.0 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 13.0 3.09716 12.0 11.0 4.9405 7.0 snp 1.0 56.44 80.5 26.16 0.0 2.0 0.5 4.0 -0.469 0.0 True 45.0 4.7712 1.217 2.0 0.5 60.0 0.0 12.1 -0.49 0.425 0.0 1.0 1.0 2.0 0.5 36.74 0.0 60.0 60.0 0.0 0.0 2.0 1.0 21.3277 0.0 1.0 0.888889 0.0 0.0 0.0 0.0 0.0 925.0 12.39 654.0 18.0 8.0 10.0459 7.35324 17.0 1.0 0.2 13.0 3.09716 12.0 4759 DOWNSTREAM NONE processed_transcript MROH7 MODIFIER ENST00000472987 0.596 11.0 4.9405 7.0 snp SNP COSV59872425 1.0 83.0 GATK-freebayes 1.0 A downstream_gene_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000472987.5 processed_transcript n.*4759G>A 4759
@ col_name=extra_vcf_info__ABHom tok=1.0 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__AC tok=2.0 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__AF tok=0.5 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__AN tok=4.0 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__DP tok=1.0 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__ExcessHet tok=0.7918 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__FS tok=0.0 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__GC tok=59.41 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__GQxMEAN tok=12.0 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__GQxSTDDEV tok=12.73 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__HCallerAC tok=2.0 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__HCallerAF tok=0.5 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__HCallerAN tok=4.0 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__HCallerDP tok=7.0 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__HCallerExcessHet tok=0.7918 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__HCallerFS tok=0.0 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__HCallerMLEAC tok=1.0 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__HCallerMLEAF tok=0.25 l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
@ col_name=extra_vcf_info__HCallerMQ tok=nan l=9815 1.0 2.0 0.5 4.0 1.0 0.7918 0.0 59.41 12.0 12.73 2.0 0.5 4.0 7.0 0.7918 0.0 1.0 0.25 nan 0.693 0.0 1.0 0.25 inf 0.0 0.0 0.0 0.0 34.59 INTRON 5 NONE nonsense_mediated_decay MROH7 MODIFIER ENST00000440047 1.609 001 SNP GATK T intron_variant MODIFIER MROH7 ENSG00000184313 transcript ENST00000440047.5 nonsense_mediated_decay 5/22 c.1390-118A>T
Traceback (most recent call last):
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/cravat_class.py", line 382, in main
self.result_path = self.run_aggregator()
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/cravat_class.py", line 905, in run_aggregator
v_aggregator.run()
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/aggregator.py", line 141, in run
for lnum, line, rd in reader.loop_data():
File "/data/umcg-mterpstra/apps/software/open-cravat/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/cravat/inout.py", line 156, in loop_data
tok = json.loads(tok)
File "/software/software/Python/3.6.4-foss-2018a/lib/python3.6/json/__init__.py", line 354, in loads
return _default_decoder.decode(s)
File "/software/software/Python/3.6.4-foss-2018a/lib/python3.6/json/decoder.py", line 339, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/software/software/Python/3.6.4-foss-2018a/lib/python3.6/json/decoder.py", line 357, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
Finished with an exception. Runtime: 9178.057s
Check /scratch/umcg-mterpstra/projects/GenomeScan104071_002/VariantAnnotation/oc/GenomeScan104071_002.n_002.annot.vcf.snpsiftdbnsfp.vcf.log
Should i also grep the vcf around this position? (thanks for your time btw)
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rkimoakbioinformatics
commented on May 31, 2024
Thanks for the information. The reason of exception was that HCallerMQ was defined as float numbers but some variants had nan as its value. OpenCRAVAT tried to parse it as a number and failed. As a user, what would be a sensible value in this case? It can be just a blank without a value, for example?
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kmoad
commented on May 31, 2024
Also, I noticed that you're having some errors with the hgvs annotator. In newer versions of OpenCRAVAT, we've moved hgvs annotation into the default mapper module, and improved it beyond what's available in the old hgvs annotator. If you update OC and run oc module update, you should get the new hgvs handling.
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mmterpstra
commented on May 31, 2024
Thanks for the great responses.
@rkiminsilico:Blank without value shoud be good For your internal data structure I don't know. The data not always has this value due to being a merge of multiple datasets.for example the only called in freebayes variants should not contain these values.
Vcf files should contain HCallerMQ=. or omit the tag altogether. For validating you can use GATK validate vcf output:https://gatk.broadinstitute.org/hc/en-us/articles/360047217931-ValidateVariants also the tag is for each ALT variant so this this is also possible 'HCallerMQ=40,.'
@kmoad: I'll update and then look at the software again.
if the rkiminsilico part is fixed you might consider closing this issue
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