unexpected char in string error

[ChristyPeterson]

Hi Chad,

I'm trying to run panseq on some publically available genomes, and was successful when running the genomes from a subspecies. As soon as I included two other subspecies, I get an "unexpected char in string" error. Weirdly, this error is coming up in strains that were successful in the first run. Those characters do not exist in the input so I'm assuming its in a temp file the program is writing and then referring back to?

Below is an example from the Master log file (the top and bottom).

2019/12/10 14:29:27 INFO |  NovelIterator.pm:186> We have 74 genomes this run 
1: PREPARING DATA
1: PREPARING DATA
1: PREPARING DATA
1: PREPARING DATA
1: PREPARING DATA
1: PREPARING DATA
1: PREPARING DATA
1: PREPARING DATA
1: PREPARING DATA
1: PREPARING DATA
1: PREPARING DATA
1: PREPARING DATA
1: PREPARING DATA
1: PREPARING DATA
Unexpected character `7' in string NZ_CP016054.1_Treponema_pallidum_subsp._pallidum_strain_PT_SIF1127_genome
Unexpected character `4' in string NZ_CP016054.1_Treponema_pallidum_subsp._pallidum_strain_PT_SIF1127_genome
Unexpected character `4' in string NZ_CP016054.1_Treponema_pallidum_subsp._pallidum_strain_PT_SIF1127_genome


Unexpected character `.' in string NZ_CP016054.1_Treponema_pallidum_subsp._pallidum_strain_PT_SIF1127_genome_(1138930..1144388)
2019/12/10 14:30:00 WARN |  CombineFilesIntoSingleFile.pm:83> Skipping /PATH/vpd/syphilis/panseq/run2-all-strains/6665952b07be10cc3db02af26d6d6f3a_5616179e4a49b14a8e4caa454f9b6f58_NR as it has size of 0 
2019/12/10 14:30:00 INFO |  Panseq.pm:268> Panseq mode set as pan 
2019/12/10 14:30:00 INFO |  SegmentMaker.pm:164> Segmenting /PATH/vpd/syphilis/panseq/run2-all-strains/6665952b07be10cc3db02af26d6d6f3a_5616179e4a49b14a8e4caa454f9b6f58 into 500bp segments 

If I remove the isolate from the analysis I get even more of these errors, for several other isolates. Any insight would be awesome.

Thanks! -Christy