Empty matrix files

[sophiakenney]

Hello,

I am running PhaME on around 2100 Salmonella genome assemblies and it runs without any error/interruption; however, all of the snp matrix files are empty except for the genome file names. All other intermediate and final output files seem unaffected by whatever the issue is for the matrix files.

Thank you in advance for your help

Sophia

[mshakya]

Hi, would you be able to share your log and ctl file? Thanks.

[sophiakenney]

Please find the requested attached. The ctl file was extension was rename to txt to allow upload.

phame.txt
dubphylo.log

Thank you

[mshakya]

hi, sorry for not getting back to you earlier. The log file looks like its not complete. Did you get anything in the alignment files? or those are empty as well?

[sophiakenney]

The alignment files are not empty.

I also ran into this same issue (empty matrix) with another dataset and also had no issues with the alignment files being created.

[mshakya]

thanks..It would be great if you can provide few more info so that i can try to replicate that issue here. You can either email me or just share it here.

• your control file.
• Genomes fasta for reference genome and few (5-6) other genomes (just accession IDs if they are from GenBank/RefSeq)
• and confirmation that you are using the master branch phame from this github.

[sophiakenney]

The reference (LT2 files) and other genomes are in the attached zip file. The control file is above (saved as phame.txt), and I am using the master branch from this github.

fasta.zip

Thank you!