No sequence data in core_gene_alignment.aln

[haruosuz]

6163695.zip

Attached is a result of comparing four plasmid sequences (CP062120 U67194 AB231906 AM261282) using roary:

roary -p $(getconf _NPROCESSORS_ONLN) -f ${roary_dir} -e -n -i 90 -s -z -cd 100 -v ${in_dir}/*.gff

There were 4 Core genes. However, there was No sequence data in core_gene_alignment.aln. I wonder if this is a bug or something?

$cat summary_statistics.txt 
Core genes      (100% <= strains <= 100%)       4

Intersection of genes (core genes) was extracted using:

query_pan_genome -g ${roary_dir}/clustered_proteins -a intersection \
 -o my_core_genes_allset.txt ${in_dir}/*.gff

$cat my_core_genes_allset.txt
group_5: AB231906.2_00021       AM261282.1_00055        CP062120.1_00019        U67194.4_00005
group_3: AB231906.2_00043       AM261282.1_00007        CP062120.1_00096        U67194.4_00026
group_12: AB231906.2_00042      AM261282.1_00006        CP062120.1_00097        U67194.4_00025
group_10: AB231906.2_00009      AM261282.1_00044        CP062120.1_00033        U67194.4_00048

I wonder if "core genes" are genes present in a single copy in every genome. There were 2 or more sequences in the alignment for the 4 Core genes.

pan_genome_sequences/

$grep -c "^>" {group_5,group_3,group_12,group_10}.fa.aln
group_5.fa.aln:5
group_3.fa.aln:7
group_12.fa.aln:5
group_10.fa.aln:5

$grep "CP062120.1" {group_5,group_3,group_12,group_10}.fa.aln
group_5.fa.aln:>CP062120.1_00019
group_5.fa.aln:>CP062120.1_00159
group_3.fa.aln:>CP062120.1_00096
group_3.fa.aln:>CP062120.1_00212
group_3.fa.aln:>CP062120.1_00213
group_3.fa.aln:>CP062120.1_00214
group_12.fa.aln:>CP062120.1_00097
group_12.fa.aln:>CP062120.1_00216
group_10.fa.aln:>CP062120.1_00033
group_10.fa.aln:>CP062120.1_00172

[magnusmanske]

we currently do not have the resources to provide support for Roary