Hi. I activated qiime 2 2019, prepared a folder named '6 sample file' to try data import which has metadata, manifest, and 6 data sequences as in the picture. I received this error. maybe as manifest and metadata are not qza (I read the tutorial but could not find how to convert into qza. Thanks a lot
There was a problem with the command:
(1/1?) no such option: -q
(qiime2-2019.7) a-PC:~ hebahussein$
(qiime2-2019.7) a-PC:~ hebahussein$ qiime tools import \
input file's name should be complete i.e. 6 sample manifest.csv. If this doesn't work, then please try converting .csv into .txt. I am not sure if .csv is an accepted file, hence, incase if problem still persists after using the complete name then you need to convert the format and see what happens.
I see that t you are working in the virtual environment? Could you please try using this command and see what happens:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /6 sample file/6 sample manifest.csv
--output-path /6 sample file/paired-end-demux.qza
--input-format PairedEndFastqManifestPhred64V2
The above should help. If this doesn't work then please convert the .csv file into .txt and repeat the above commands by using the .txt file name.
I read the tutorial many times but still get errors. Do I need to make a folder with metadata file and manifest file only to import to qiime? Do I need to include in the folder the individual FASTQ files (2 per each sample) as attached in the picture? What are the required format of all the files? I have metadata in yml, manifest in excel or CSV, and individual sequence files in qz extension. Anyone has the exact codes to import these files for quality analysis and denosing? I am struggling with this step for too long and tried many extensions so will appreciate your help.
I merged these two topics because they seem to be addressing the same problem. This is a gentle reminder to try and keep topics together; it makes it easier for everyone to use the forum and keeps things consistent.
You have to do a little work, you have to replace the filepath where I wrote "/NEEDS/FULL/FILEPATH/" Ben
edit: the forward and reverse file has to be in the same row - sampleID i am assuming Rahe001-UC etc. I am assuming this is an ulcerative colitis study?
The command in Qiime2 should direct to this manifest.txt file - the manifest.txt will tell QIIME2 where to find the files.
To answer your questions:
They are 12 individidual files - they just happen to be forward and reverse for 1 sample
You should use what format you like, I use TXT tab delimited as it is what I was trained in and what i know.
Again, I should reemphasize, these are still 12 files, but QIIME2 needs to know that they belong to 6 samples.
Thanks so I need to write the full path for each individual file? also, to import to qiime, shall I import this manifest file as txt and metadata as yml? no need for the 12 individual files for 6 samples (6 forward and 6 reverse)?
no not ulcerative colitis. I dont know how to make the forward and reverse in same row and when I write the path, shall i write it wish slashes as you did?
Yes, remember I showed you a trick to find the full path name, if not, it's right clicking on a file in a MAC then HOLDING alt/option you have an option of selecting the full filepath. Ben
Thanks ben. I changed the extension to txt. I made the reverse and forward in one line. I added the path. I pasted this code in qiime environment and got this error. I am attaching the screenshots unzip -q pe-64.zip
the error I got:
There were some problems with the command:
(1/2) Invalid value for "--input-path": Path "/Users/hebahussein/Desktop/6"
does not exist.
(2/2) Got unexpected extra arguments (sample import)
(qiime2-2019.7) a-PC:~ hebahussein$
thanks. I changed the extension to txt. I made the reverse and forward in one line. I added the path. I pasted this code in qiime environment and got this error. I am attaching the screenshots unzip -q pe-64.zip
the error I got:
There were some problems with the command:
(1/2) Invalid value for "--input-path": Path "/Users/hebahussein/Desktop/6"
does not exist.
(2/2) Got unexpected extra arguments (sample import)
(qiime2-2019.7) a-PC:~ hebahussein$
thanks Yes I did remove all spaces from the manifest file and even changed the folder into one word so no need for dashes or spaces and got same errors. Do I need to mkdir new folder and and change directory to it and put: metadata: 12 file sequence: and manifest? I even tried and did not work. There were some problems with the command:
yes how to know which slash? also, I will remake the manifest file. maybe when we changed the name of the manifest file and folder and removed the spaces, it did not recognize them
