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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Invalid seed issue #147

Closed brenna-levine closed 3 years ago

brenna-levine commented 3 years ago

Hi, I'm keep getting the invalid seed message when I use the "mito" program, regardless of the seed that I use (I have tried many). I know my files have mitochondrial reads in them, as I have previously aligned these to a reference genome, and that I have high coverage. Here is my log file (the extended doesn't seem to have much information in it):

Project:

Project name = test Type = mito Genome range = 12000-22000 K-mer = 33 Max memory = Extended log = 1 Save assembled reads = no Seed Input = sequence.fasta Extend seed directly = no Reference sequence = Variance detection = Chloroplast sequence =

Dataset 1:

Read Length = 250 Insert size = 500 Platform = illumina Single/Paired = PE Combined reads = Forward reads = reads_1.fastq Reverse reads = reads_2.fastq

Heteroplasmy:

Heteroplasmy = HP exclude list = PCR-free =

Optional:

Insert size auto = yes Use Quality Scores =

Subsampled fraction: 90.97 % Forward reads without pair: 26 Reverse reads without pair: 0

Retrieve Seed...

INVALID SEED, PLEASE TRY AGAIN WITH A NEW ONE

The seed is:

MT882033.1 CAAAGGTAGCATAATAATTTGTTTTTTAATTGGAAACTAGTATGAATGGTCATACGAGGGATTGACTTTC TTTATCTTACTTAAATTAATTTTATTTTTCTGTGAAAAAGCAGAGATTTCATTAGTAGACGATAAGACCC TTTAAAACTTTATTCATTATAGAAGTATAATTTTGTTAGGTTTTAATAGTGTACTTTTTTAATGAGTTTT GTTGGGGCGACAGGTAAATTTATTTAACTTTATTTTTGTTTTTCACTAATTAGTGTTTATTTGATCCAGA TTTAGTTTTGATTATAAGTTTAAGTTACTT Can you advise?

Thanks,

Brenna

ndierckx commented 3 years ago

I saw you just closed it when I was looking :) But sorry, I can't tell what the problem is from this log file..