SeqSero2 was silently failing (returning no match) on a FASTQ file using the assembly method.
This was caused by a SPAdes error due to an inability to determine the Q-score offset for the FASTQ files.
By default SPAdes automatically determines the phred-score offset from the FASTQ file and fails when it can't. I added an option to set the --phred-offset option to SPAdes on the SeqSero2_package.py commandline and pass it to spades.py.
SeqSero2 was silently failing (returning no match) on a FASTQ file using the assembly method.
This was caused by a SPAdes error due to an inability to determine the Q-score offset for the FASTQ files.
By default SPAdes automatically determines the phred-score offset from the FASTQ file and fails when it can't. I added an option to set the
--phred-offsetoption to SPAdes on theSeqSero2_package.pycommandline and pass it tospades.py.