Error:ref seq seems to be aligned
Closed this issue · 5 comments
Hi,
I am trying to align a sequence I pulled from Genbank with two draft isolate genomes that are in a directory. Unfortunately, when I run this, I get the error ref seq seems to be aligned. Syntax below:
/Users/tadediran/Desktop/Parsnp-OSX64-v1.2/parsnp -r /Users/tadediran/Desktop/Parsnp-OSX64-v1.2/Clade_Pair_SNP_analysis/Clade3_all/usa400_annotation.fasta -d /Users/tadediran/Desktop/Parsnp-OSX64-v1.2/Clade_Pair_SNP_analysis/Clade3_all/All_pair_data/
Any help would be appreciated
@tadediran can you please attach the full output of parsnp? And can you confirm that there are no gaps (-) characters in your reference sequence?
-Bryce
|--Parsnp v1.2--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
SETTINGS:
|-refgenome: /Users/tadediran/Desktop/Parsnp-OSX64-v1.2/Clade_Pair_SNP_analysis/Clade3/GCA_002795285.1_ASM279528v1_genomic.fna
|-aligner: libMUSCLE
|-seqdir: /Users/tadediran/Desktop/Parsnp-OSX64-v1.2/Clade_Pair_SNP_analysis/Clade3/MRSA297_6GL/
|-outdir: /Users/tadediran/Desktop/Parsnp-OSX64-v1.2/Clade_Pair_SNP_analysis/Clade3/Clade3_pair_analysis/P_2020_09_17_222317042309
|-OS: Darwin
|-threads: 32
<>
-->Reading Genome (asm, fasta) files from /Users/tadediran/Desktop/Parsnp-OSX64-v1.2/Clade_Pair_SNP_analysis/Clade3/MRSA297_6GL/..
|->[OK]
-->Reading Genbank file(s) for reference (.gbk) ..
|->[WARNING]: no genbank file provided for reference annotations, skipping..
ERROR: ref genome sequence /Users/tadediran/Desktop/Parsnp-OSX64-v1.2/Clade_Pair_SNP_analysis/Clade3/GCA_002795285.1_ASM279528v1_genomic.fna seems to aligned! remove and restart
@tadediran It looks like you are using an older version of parsnp which is not supported, would you please update to the most recent version? Our latest version, 1.5.3, is available on bioconda
Unfortunately, I am getting the same error as before
Hi @tadediran! Could you share the output from v1.5.3? And can you confirm that there are no gap characters - in the reference sequence?