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marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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Error:ref seq seems to be aligned #84

Closed tadediran closed 3 years ago

tadediran commented 3 years ago

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

bkille commented 3 years ago

@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

tadediran commented 3 years ago

|--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

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-->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

bkille commented 3 years ago

@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

tadediran commented 3 years ago

Unfortunately, I am getting the same error as before

bkille commented 3 years ago

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?