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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Single end reads error-No input file found, make sure it are fastq files No such file or directory #213

Open dimserg opened 9 months ago

dimserg commented 9 months ago

Hello,

thank you for this valuable tool! I am trying to run a chloroplast assembly using SE reads and I am getting this error every time:

No input file found, make sure it are fastq files No such file or directory

I am giving the directory of the single reads file in the "Forward reads" in the config.txt file. Here is my config.txt. Is there something I am missing because I am trying to use single end reads?

Thank you!

Project:

Project name = 311_chloro Type = chloro Genome Range = 120000-180000 K-mer = 39 Max memory = 8 Extended log = Save assembled reads = Seed Input = /home/projects/dimser/NovoPlasty/seed.fasta Extend seed directly = Reference sequence = Variance detection = Chloroplast sequence =

Dataset 1:

Read Length = 151 Insert size = 300 Platform = illumina Single/Paired = SE Combined reads = Forward reads = /home/projects/dimser/NovoPlasty/single_reads/311_sigle.fastq Reverse reads = Store Hash =

Heteroplasmy:

MAF = HP exclude list = PCR-free =

Optional:

Insert size auto = yes Use Quality Scores = no Reduce ambigious N's = Output path =

ndierckx commented 9 months ago

Hi, If you use the SE mode you should put the fastq path under the combined reads.