No exon_id in mouse mm9 ensembl annotaiotn

[weizhu365]

There is no exon_id in the mouse mm9 annotation.
head Mus_musculus.NCBIM37.67.gtf
NT_166433 protein_coding exon 11955 12166 . + . gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "1"; gene_name "AC007307.1"; gene_biotype "protein_coding"; transcript_name "AC007307.1-201";
NT_166433 protein_coding CDS 12026 12166 . + 0 gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "1"; gene_name "AC007307.1"; gene_biotype "protein_coding"; transcript_name "AC007307.1-201"; protein_id "ENSMUSP00000100851";
NT_166433 protein_coding start_codon 12026 12028 . + 0 gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "1"; gene_name "AC007307.1"; gene_biotype "protein_coding"; transcript_name "AC007307.1-201";
NT_166433 protein_coding exon 16677 16841 . + . gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "2"; gene_name "AC007307.1"; gene_biotype "protein_coding"; transcript_name "AC007307.1-201";
NT_166433 protein_coding CDS 16677 16841 . + 0 gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "2"; gene_name "AC007307.1"; gene_biotype "protein_coding"; transcript_name "AC007307.1-201"; protein_id "ENSMUSP00000100851";
NT_166433 protein_coding exon 17745 17814 . + . gene_id "ENSMUSG00000000702"; transcript_id "ENSMUST00000105216"; exon_number "3"; gene_name "AC007307.1"; gene_biotype "protein_coding"; transcript_name "AC007307.1-201";

So, I got error while try to running isovar (see below):
isovar-protein-sequences.py --vcf batch1-ensemble-annotated-decomposed.vcf --bam ERR420397.fastq.genome.sorted.bam --min-alt-rna-reads 2 --protein-sequence-length 30 --output rep1-results.csv --genome NCBIM37
2018-03-08 21:59:24,270 - isovar.allele_reads:200 - INFO - Gathering reads for Variant(contig='1', start=4336591, ref='', alt='T', reference_name='NCBIM37')
2018-03-08 21:59:24,289 - isovar.allele_reads:208 - INFO - Gathering variant reads for variant Variant(contig='1', start=4336591, ref='', alt='T', reference_name='NCBIM37') (chromosome = 1, gene names = ['Rp1'])
2018-03-08 21:59:24,303 - isovar.locus_reads:314 - INFO - Found 0 reads overlapping locus 1: 4336591-4336592
2018-03-08 21:59:24,303 - isovar.translation:461 - INFO - No supporting reads for variant Variant(contig='1', start=4336591, ref='', alt='T', reference_name='NCBIM37')
2018-03-08 21:59:24,303 - isovar.allele_reads:200 - INFO - Gathering reads for Variant(contig='1', start=5088129, ref='A', alt='C', reference_name='NCBIM37')
2018-03-08 21:59:24,305 - isovar.allele_reads:208 - INFO - Gathering variant reads for variant Variant(contig='1', start=5088129, ref='A', alt='C', reference_name='NCBIM37') (chromosome = 1, gene names = ['Atp6v1h'])
2018-03-08 21:59:24,318 - isovar.locus_reads:314 - INFO - Found 22 reads overlapping locus 1: 5088128-5088130
2018-03-08 21:59:24,318 - isovar.variant_sequences:422 - INFO - Initial pool of 2 variant sequences (min length=50, max length=50)
2018-03-08 21:59:24,318 - isovar.assembly:140 - INFO - Collapsed 2 -> 2 sequences
2018-03-08 21:59:24,318 - isovar.variant_sequences:440 - INFO - After overlap assembly: 1 variant sequences (min length=56, max length=56)
2018-03-08 21:59:24,320 - isovar.variant_sequences:207 - INFO - Coverage: [1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1] (len=56)
2018-03-08 21:59:24,320 - isovar.variant_sequences:330 - INFO - Kept 1/1 variant sequences after read coverage trimming to >=2x
2018-03-08 21:59:24,320 - isovar.variant_sequences:456 - INFO - After coverage & length filtering: 1 variant sequences (min length=44, max length=44)
2018-03-08 21:59:24,636 - pyensembl.sequence_data:118 - INFO - Loaded sequence dictionary from /home/zhuwe/.cache/pyensembl/NCBIM37/ensembl67/Mus_musculus.NCBIM37.67.cdna.all.fa.gz.pickle
2018-03-08 21:59:24,653 - pyensembl.sequence_data:118 - INFO - Loaded sequence dictionary from /home/zhuwe/.cache/pyensembl/NCBIM37/ensembl67/Mus_musculus.NCBIM37.67.ncrna.fa.gz.pickle
2018-03-08 21:59:24,666 - pyensembl.database:436 - WARNING - Encountered error "no such column: exon_id" from query "
SELECT exon_number, exon_id
FROM exon
WHERE transcript_id = ?
" with parameters ['ENSMUST00000044369']
Traceback (most recent call last):
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/pyensembl/common.py", line 65, in wrapped_fn
return cache[cache_key]
KeyError: (<pyensembl.database.Database object at 0x7fffec08ba20>, ('exon_number', 'exon_id'), ('feature', 'exon'), ('filter_column', 'transcript_id'), ('filter_value', 'ENSMUST00000044369'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/bioinfo/packages/anaconda3/bin/isovar-protein-sequences.py", line 46, in
df = protein_sequences_dataframe_from_args(args)
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/isovar/cli/protein_sequences.py", line 73, in protein_sequences_dataframe_from_args
return protein_sequences_generator_to_dataframe(protein_sequences_generator)
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/isovar/protein_sequences.py", line 323, in protein_sequences_generator_to_dataframe
gene=lambda x: ";".join(x)))
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/isovar/dataframe_builder.py", line 189, in dataframe_from_generator
for variant, elements in variant_and_elements_generator:
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/isovar/protein_sequences.py", line 279, in reads_generator_to_protein_sequences_generator
variant_sequence_assembly=variant_sequence_assembly)
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/isovar/translation.py", line 492, in translate_variant_reads
transcript_id_whitelist=transcript_id_whitelist)
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/isovar/reference_context.py", line 117, in reference_contexts_for_variant
transcript_id_whitelist=transcript_id_whitelist)
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/isovar/effect_prediction.py", line 95, in reference_transcripts_for_variant
transcript_id_whitelist=transcript_id_whitelist)
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/isovar/effect_prediction.py", line 44, in predicted_coding_effects_with_mutant_sequence
if not transcript.complete:
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/memoized_property.py", line 40, in fget_memoized
setattr(self, attr_name, fget(self))
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/pyensembl/transcript.py", line 393, in complete
self.coding_sequence is not None and
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/memoized_property.py", line 40, in fget_memoized
setattr(self, attr_name, fget(self))
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/pyensembl/transcript.py", line 435, in coding_sequence
start = self.first_start_codon_spliced_offset
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/memoized_property.py", line 40, in fget_memoized
setattr(self, attr_name, fget(self))
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/pyensembl/transcript.py", line 414, in first_start_codon_spliced_offset
start_offsets = self.start_codon_spliced_offsets
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/memoized_property.py", line 40, in fget_memoized
setattr(self, attr_name, fget(self))
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/pyensembl/transcript.py", line 359, in start_codon_spliced_offsets
in self.start_codon_positions
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/pyensembl/transcript.py", line 358, in
for position
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/pyensembl/transcript.py", line 293, in spliced_offset
for exon in self.exons:
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/pyensembl/transcript.py", line 121, in exons
feature="exon")
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/pyensembl/common.py", line 67, in wrapped_fn
value = fn(*args, **kwargs)
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/pyensembl/database.py", line 469, in query
sql, required=required, query_params=query_params)
File "/bioinfo/packages/anaconda3/lib/python3.6/site-packages/pyensembl/database.py", line 429, in run_sql_query
cursor = self.connection.execute(sql, query_params)
sqlite3.OperationalError: no such column: exon_id

end of the error message

Is there any fix for this problem?

Thanks,

Wei