diff --git a/Rfam/Lib/Bio/Rfam/Utils.pm b/Rfam/Lib/Bio/Rfam/Utils.pm index 56c502f6..ad6a19a7 100644 --- a/Rfam/Lib/Bio/Rfam/Utils.pm +++ b/Rfam/Lib/Bio/Rfam/Utils.pm @@ -2628,7 +2628,7 @@ sub genbank_fetch_seq_info { } $info_HHR->{$accver}{"length"} = $length; - # for taxid and mol_type, we have to fetch from Quailifier_values, and may have more than 1 + # for taxid and mol_type, we have to fetch from Qualifier_values, and may have more than 1 # in that case, they will be concatenated together my $taxid_val = $gbseq->findvalue('./GBSeq_feature-table/GBFeature/GBFeature_quals/GBQualifier/GBQualifier_value[starts-with(text(), "taxon:")]'); my $taxid = undef; @@ -2643,7 +2643,11 @@ sub genbank_fetch_seq_info { $taxid = $cur_taxid; } elsif($cur_taxid != $taxid) { - croak "ERROR in $sub_name for $accver, > 1 taxids read: $taxid and $cur_taxid\nFull taxon values read: $orig_taxid_val\n"; + ; # do nothing, see comment below + # Change Jan 29, 2021: if multiple taxids are returned for a single accession, + # always use the first one and don't complain. Previously we would fail here + # with following croak: + #croak "ERROR in $sub_name for $accver, > 1 taxids read: $taxid and $cur_taxid\nFull taxon values read: $orig_taxid_val\n"; } $taxid_val =~ s/^taxon\:(\d+)//; }