search

zwets / ident-16s

Rapid identification of bacterial species from FASTA contigs
GNU General Public License v3.0
2 stars 1 forks source link

running error #1

Open aslangabriel opened 4 months ago

aslangabriel commented 4 months ago

Hi, I ran the command "./ident-16s hpsM15.fa.gz", the error was listed as follows“# 16S_rRNA_1_Origin_hpsM15 (uf:cut:1:470) Error: NCBI C++ Exception: T0 "/build/ncbi-blast+-S1iyIZ/ncbi-blast+-2.9.0/c++/src/serial/objistrasnb.cpp", line 499: Error: byte 81: overflow error ( at [].[].gi) T0 "/build/ncbi-blast+-S1iyIZ/ncbi-blast+-2.9.0/c++/src/serial/member.cpp", line 769: Error: ncbi::CMemberInfoFunctions::ReadWithSetFlagMember() - error while reading seqid ( at Blast-def-line-set.[].[].seqid.[].[].gi)”

zwets commented 3 months ago

The error message from blast "error while reading seqid ( at Blast-def-line-set.[].[].seqid.[].[].gi)” seems to indicate that it fails to parse the sequence identifier, i.e. the bit right after '>' on the defline of a sequence.

However, the first line of your output suggests that the defline in your fasta file is OK. What is the output when you run ident-16s with the -v (verbose) flag?

./ident-16s -v hpsM15.fa.gz

To check if the issue isn't with your 16S database:

blastdbcheck -db 16S_ribosomal_RNA -legacy -must_have_taxids -full