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cmayer / MitoGeneExtractor

The MitoGeneExtractor can be used to extract protein coding mitochondrial genes, such as COI and others from short and long read sequencing libraries.
GNU Affero General Public License v3.0
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Fastq file could not be opened #16

Open jrpletch opened 5 days ago

jrpletch commented 5 days ago

Hello, I am trying to extract COI genes from raw Illumina sequences of cestodes to try and ID the hosts. I am using the cestodes as a proof of concept but would eventually like to try it with whole genome sequences from fleas to see what other sequences we might incidentally capture such as hosts, other parasites, or contaminants. I managed to extract a vole mitogenome from this data using Novoplasty, but would like to find a way to ID other potential sequences and it looked like MitoGeneExtractor could be the way to go. I managed to get MitoGeneExtractor installed but got this error after trying to run it with my data. I'm just starting to learn all this so it is entirely possible I'm missing something obvious. I did have to reverse the direction of the slashes in the file paths, initially they were \ but they ended up all disappearing after I ran the command.

This is what I ran:

./MitoGeneExtractor-v1.9.5 -q D:/NovoplastyPractice_Josh/A013489/A013489_L000_R1_001.fastq/A013489_L000_R1_001.fastq -q D:/NovoplastyPractice_Josh/A013489/A013489_L000_R2_001.fastq/A013489_L000_R2_001.fastq -p mammalia_COI_genera_consensus -o A013489_mammal_alignment.fas -n 0 -c A013489_mammal_consensus.fas -t 0.5 -r 1 -C 2

Thanks, Josh

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marievalerie commented 4 days ago

Hello, Are you sure your file path is correct? It looks like that you've specified the file name twice i.e. your files are located in a directory that has the same name as your file?