Entering edit mode
4.9 years ago
hellen6570
▴
10
Hi all,
I got some fastq files from nanopore and trying to blast to a custom database.
So first, I build a database:
makeblastdb -in sh_general_release_dynamic_02.02.2019.fasta -dbtype nucl -out UniteBlast
Building a new DB, current time: 04/25/2019 15:41:39
New DB name: /igbgroup/a-m/henganl2/Unite/UniteBlast
New DB title: UniteBlast
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 35667 sequences in 1.76276 seconds.
Then, when I try to use -blastn
blastn -query BC15.fastq -db /igbgroup/a-m/henganl2/Unite/UniteBlast -task blastn -outfmt 6 -out BC15_B.xml
I got the following error:
CFastaReader: Hyphens are invalid and will be ignored around line 1`FASTA-Reader: Ignoring invalid residues at position(s): On line 1: 1-5, 7-9, 11, 16, 18-19, 21-24, 26-28, 30-37, 42, 44, 49, 51-60, 62-65, 68-71, 73, 76-77, 79-84, 89-92, 94, 96, 98, 100, 102-103, 106, 109-114, 118-120, 127, 129, 131-136, 138-139, 141-142, 144-152
` Can anyone help me out? Thanks!!