sqlalchemy.exc.InterfaceError: (sqlite3.InterfaceError) Error binding parameter 51

I am currently using gemini 0.18.3 because I didn’t want to break my installation. My command is:

gemini_python /mnt/isilon/cbmi/variome/bin/vcf2db/vcf2db.py --legacy-compression vcfs/sample.snpeff.anno.vcf.gz sample.pedfile gemini/test.db

Here are the config files that I used in vcfanno: vcfanno.conf

[[annotation]]
file = "ExAC.r0.3.sites.vep.tidy.vcf.gz"
fields = ["AC_Adj", "AN_Adj"]
names = ["exac_ac_all", "exac_an_all"]
ops = ["self", "self"]

[[annotation]]
file = "/home/rathik/grin_test/GRCh38/annotations/dbsnp137.coding.variants.sift.prediction.bed.gz"
columns = [14,15,18,19]
names = ["Provean_score","Provean_prediction","SIFT_score","SIFT_prediction"]
ops     = ["self", "self", "self", "self"]

[[annotation]]
file = "ESP6500SI.all.snps_indels.tidy.v2.vcf.gz"
fields = ["FG","AAC", "PH"]
names = ["functionGVS", "aminoAcidChange", "polyPhen"]
ops = ["self", "self", "self"]

[[annotation]]
file = "/home/rathik/grin_test/GRCh38/annotations/literaturegenes_GRCh38.bed.gz"
columns = [4]
names = ["literature_genes"]
ops = ["self"]

[[annotation]]
file = "/home/rathik/grin_test/GRCh38/annotations/recurrentgenes_GRCh38.bed.gz"
columns = [4]
names = ["recurrent_genes"]
ops = ["self"]

[[annotation]]
file = "/home/rathik/grin_test/GRCh38/annotations/rvis_GRCh38.bed.gz"
columns = [4,5]
names = ["rvis_genes","rvis_score"]
ops = ["self","self"]

[[postannotation]]
fields = ["exac_ac_all", "exac_an_all"]
name = "exac_af_all"
op = "lua:divfunc(exac_ac_all[1],exac_an_all)"
type = "Float"

vcfanno.lua

function divfunc(a, b)
        if(a == 0) then 
                return 0.0
        else 
        return string.format("%.9f", a / b)
    end
end

Even though I am getting the following error, a database is created:

setting exac_af_all to Type String because it has Number=.
/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:185: SAWarning: Unicode type received non-unicode bind param value 'NLES10'. (this warning may be suppressed after 10 occurrences)
  (util.ellipses_string(value),))
/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:185: SAWarning: Unicode type received non-unicode bind param value '733459'. (this warning may be suppressed after 10 occurrences)
  (util.ellipses_string(value),))
/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:185: SAWarning: Unicode type received non-unicode bind param value '733482'. (this warning may be suppressed after 10 occurrences)
  (util.ellipses_string(value),))
/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:185: SAWarning: Unicode type received non-unicode bind param value '733434'. (this warning may be suppressed after 10 occurrences)
  (util.ellipses_string(value),))
/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:185: SAWarning: Unicode type received non-unicode bind param value '1'. (this warning may be suppressed after 10 occurrences)
  (util.ellipses_string(value),))
10000 variant_impacts:44264 effects time: 7.6   chunk time:13.6 734.00 variants/second
20000 variant_impacts:43003 effects time: 7.2   chunk time:12.5 764.97 variants/second
30000 variant_impacts:42482 effects time: 7.4   chunk time:11.4 798.41 variants/second
40000 variant_impacts:45072 effects time: 7.3   chunk time:12.4 801.17 variants/second
50000 variant_impacts:54559 effects time: 8.7   chunk time:14.3 777.96 variants/second
60000 variant_impacts:48911 effects time: 7.9   chunk time:13.3 773.14 variants/second
70000 variant_impacts:40810 effects time: 7.2   chunk time:12.2 779.20 variants/second
80000 variant_impacts:39796 effects time: 7.0   chunk time:12.2 783.81 variants/second
90000 variant_impacts:48542 effects time: 8.1   chunk time:13.5 778.56 variants/second
100000 variant_impacts:41732    effects time: 7.2   chunk time:12.6 780.30 variants/second
Traceback (most recent call last):
  File "/mnt/isilon/cbmi/variome/bin/vcf2db/vcf2db.py", line 720, in <module>
    blobber=blobber)
  File "/mnt/isilon/cbmi/variome/bin/vcf2db/vcf2db.py", line 175, in __init__
    self.load()
  File "/mnt/isilon/cbmi/variome/bin/vcf2db/vcf2db.py", line 240, in load
    self._load(self.vcf, create=False, start=i+1)
  File "/mnt/isilon/cbmi/variome/bin/vcf2db/vcf2db.py", line 224, in _load
    self.insert(variants, expanded, keys, i)
  File "/mnt/isilon/cbmi/variome/bin/vcf2db/vcf2db.py", line 279, in insert
    vilengths, variant_impacts)
  File "/mnt/isilon/cbmi/variome/bin/vcf2db/vcf2db.py", line 307, in _insert
    self.__insert(v_objs, self.metadata.tables['variants'].insert())
  File "/mnt/isilon/cbmi/variome/bin/vcf2db/vcf2db.py", line 331, in __insert
    trans.execute(stmt, o)
  File "/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 914, in execute
    return meth(self, multiparams, params)
  File "/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement
    compiled_sql, distilled_params
  File "/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context
    context)
  File "/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1341, in _handle_dbapi_exception
    exc_info
  File "/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=cause)
  File "/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_context
    context)
  File "/mnt/isilon/cbmi/variome/bin/gemini/data/anaconda/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 450, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.InterfaceError: (sqlite3.InterfaceError) Error binding parameter 51 - probably unsupported type. 
[SQL: u'INSERT INTO variants (variant_id, chrom, start, "end", vcf_id, ref, alt, qual, filter, type, sub_type, call_rate, num_hom_ref, num_het, num_hom_alt, aaf, gene, transcript, is_exonic, is_coding, is_lof, is_splicing, exon, codon_change, aa_change, aa_length, biotype, impact, impact_so, impact_severity, polyphen_pred, polyphen_score, sift_pred, sift_score, an, baseqranksum, clippingranksum, dp, fs, lof, mq, mqranksum, nmd, provean_prediction, provean_score, qd, readposranksum, sift_prediction, sor, aminoacidchange, exac_af_all, exac_an_all, functiongvs, literature_genes, polyphen, recurrent_genes, rvis_genes, rvis_score, gts, gt_types, gt_phases, gt_depths, gt_ref_depths, gt_alt_depths, gt_quals) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)'] [parameters: (154484, 'chr11', 1016967, 1016968, None, 'T', 'G,C', 7694.89990234375, None, 'snp', 'unknown', 1.0, 0, 3, 0, 0.5, 'MUC6', 'ENST00000421673', 1, 1, 0, 0, '31', 'Aca/Cca', 'T1945P', 2439, 'protein_coding', 'missense_variant', 'missense_variant', 'MED', None, None, None, None, 6, 7.900000095367432, -0.39399999380111694, 2251, 49.323001861572266, 'None', 64.66000366210938, -2.3959999084472656, 'None', None, None, 3.430000066757202, 2.5, None, 4.144999980926514, 'None', inf, (110356, 110356), 'None', 'MUC6', 'None', None, 'MUC6', '1.26', <read-only buffer for 0x2aaac57ac7b0, size -1, offset 0 at 0x2aaac7c65eb0>, <read-only buffer for 0x2aaac57ac850, size -1, offset 0 at 0x2aaac7c653b0>, <read-only buffer for 0x2aaac57ac8f0, size -1, offset 0 at 0x2aaac7c65130>, <read-only buffer for 0x2aaac4daddf8, size -1, offset 0 at 0x2aaac7c558f0>, <read-only buffer for 0x2aaac4dadea0, size -1, offset 0 at 0x2aaac7c55930>, <read-only buffer for 0x2aaac4dadf48, size -1, offset 0 at 0x2aaac7c55970>, <read-only buffer for 0x2aaac57ac990, size -1, offset 0 at 0x2aaac7c559b0>)]

Why do the values at the end look weird?

Thanks!

[brentp]

and I’ll see how to improve the situation for cases like the one you report.

[brentp]

ok. please keep us posted. we are using the new loader as well, but you are bound to find issue we haven’t seen.