I am new to using Qiime2 on a Windows 10 Windows subsystem for linux Ubuntu system. I installed Qiime2 using the conda environment and activated it via: conda activate qiime2-2020.11. My sequences have been stripped of primer and barcodes by the Novogene sequencing facility and I have both reverse and forward sequences for each sequence installed in a sub directory (B61_1.fq.gz, B61_2.fq.gz) . After reading the most recent import guidelines I decided to import using a manifest file system. I assume that my sequences are Phred33V2. I have spent several days searching the forum for helpful information, much of which was helpful in promoting an overall understanding of importing. I chose to simplify the procedure to see if it would work on importing just one forward and reverse sequence. If that was successful, then I would be on the right track and could proceed with further imports. However, I still have a problem. I get the following error message:
(1/1) Invalid value for '--input-path': Path '/home/michaelanderson74078/practice/pe-b61-manifest.txt' is not readable.
Here is my manifest file entitled: pe-b61-manifest.txt
sample-id forward-absolute-filepath reverse-absolute-filepath
B61 /home/michaelanderson74078/practice/sequences/B61_1.fq.gz /home/michaelanderson74078/practice/sequences/B61_2.fq.gz
#my import command is as below:
qiime tools import \ --type 'SampleData[PairedEndSequencesWithQuality]' \ --input-path /home/michaelanderson74078/practice/pe-b61-manifest.txt \ --output-path /home/michaelanderson74078/practice/paired-end-demux.qza \ --input-format PairedEndFastqManifestPhred33V2
The sequences are found in a subfolder /home/michaelanderson74078/sequences/ B61_1.fq.gz or …// B61_2.fq.gz
Also when I try to open the manifest file via the nano text editor in the WSL window I get an error message:
Error reading pe-b61-manifest.txt: Permission denied.
Obviously the WSL Ubuntu system is not able to read the manifest file. The manifest file was created by Notepad++ text editor and saved as a normal txt file.
What am I missing? Am I using the right file type for the manifest file? Should I save it as a csv file type?
The import system works when I use the downloaded unzipped sequence data following all the directions. I get a legitimate qza file, but not with my sequences.
I am stuck.