$ parsnp_linux_ignoresize -r ecoli_NZ_CP027462.fasta -d . -o coregenome -x -c
|--Parsnp v1.2--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
***************************
SETTINGS:
|-refgenome: /storage/data/DATA4/analysis/Datta/CRE_outbreak/Trees/Parnsp_Gubbins_Concordant_Samples/CRE_Paola-GIS/ecoli_gte1kbContigs/ecoli_NZ_CP027462.fasta
|-aligner: libMUSCLE
|-seqdir: .
|-outdir: coregenome
|-OS: Linux
|-threads: 32
***************************
<<Parsnp started>>
-->Reading Genome (asm, fasta) files from ...
|->[OK]
-->Reading Genbank file(s) for reference (.gbk) ..
|->[WARNING]: no genbank file provided for reference annotations, skipping..
Traceback (most recent call last):
File "<string>", line 656, in <module>
IndexError: string index out of range
Solution: a previous failed run generated empty parsnp.fasta file which led to this error. By deleting parsnp.fasta fixed the script run again.
