alignment file broken?

[Lneffe]

Hi,

I have been using parSNP successfully a couple of times.
The last time I ran it on 50 K.pneumoniae genomes and it didn´t produce any error message.
But when I wanted to convert the .ggr file or .xmfa file to a mutlifasta file with harvestools it was not possible. Although I was able to open the files in ginger without problems.
The message I got is:
ERROR:LCB 634 extends beyond reference (position 47356)
When the programm tried to write the new file.
I am using the Version 1.2

Is the gingr file broken?

Thank you,
Lisa

[bkille]

@Lneffe Version 1.2 is no longer supported and unfortunately the output is rather difficult to debug 😞 I would suggest updating to the current version of parsnp and seeing if the error persists. If not, I would be happy to work through it with you!

-Bryce

[Lneffe]

Hello Bryce,

I updated parsnp to Parsnp 1.5.3. The same error presists, when using harvesttools (still old version) and trying to convert the file to fasta.

Thank you for your help!

[bkille]

@Lneffe Alright, I'll take a look and see what is going on in Harvest-tools and get back to you!

[MBiggel]

Hi,

could you solve the issue? I am running into the same problem using the latest parsnp and harvesttools releases.

Thanks!
Michael

[bkille]

If it opens fine in gingr, then I'm guessing it is a bug with harvesttools. I'll try to replicate the error, but if you attach the problem file here I'll be able to take a look at it much quicker.

[sdoms]

Hi, did anyone solve this issue? I'm having exactly the same error message and would be happy to share the problem file.
I am assuming that the problem is that aligned sequences have many fragments that are missing in the reference sequence.