Please tell me how can I import my data in Qiime2. It is puzzling in tutorial. It gives a sample we should download then unzip it, but I would like to work on my data. The command is there after two commands seems to be modified by my file name. It is just an idea! I have no any clue. I changed some parts but did not worked. By the way there are some phrases, such as INPUT, OUTPUT and TYPE are unfamiliar to me. Tell me what should I do. Thanks
Have you looked through the tutorial and played with those files to try and structure yours the same way? I find the tutorials are typically really helpful in specifying the filetypes if you work through them. The test files are presented as zipped files, since its easiest to download them, but sequence files are also usually compressed.
If you have questions about the formats, please also review the semantic types in QIIME 2, since these can be helpful to determine what you need.
Error: Invalid value for “–input-path”: Path “1.fastq.gz” does not exist.
I have still the same problem.
Is there a protocol about the format, path, etc. I got stuck this step. I tried more but could not solve it.
I asked more questions but I have to share the current problem with you.
I tried another way I got a new error ralated to format. i am not familiar with forma what is suit to it.
qiime tools import \
Traceback (most recent call last):
File “/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/util.py”, line 91, in parse_format
format_record = pm.formats[format_str]
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/tools.py”, line 146, in import_data
File “/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 206, in import_data
view_type = qiime2.sdk.parse_format(view_type)
File “/home/mpi/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/util.py”, line 93, in parse_format
raise TypeError(“No format: %s” % format_str)
TypeError: No format: dir
Since I know you’re a new user to both Linux and QIIME 2, it’s really important to learn to trouble shoot yourself. dir is not a semantic type (a valid type argument); have you read the type documentation?
Have you been able to get the tutorial to work? If you download and unzip the tutorial data, have you explored the structure (directory structure and file types) there? Those may also help you better pattern your imports.
I made .qza artifact with the data that is present in tutorial page in Casava paired end part.
I was successful! But my problem is on my data. I am unsuccessful to import it that is why I asked your team.
It seems input-format has to be modified to sth. I do not know.
I understand your frustration. You need to place all your files in a single directory, and then pass the directory in as your input-path and then pass in your format as CasavaOneEightSingleLanePerSampleDirFmt. However, it looks like your file names are not Casava-compatible, in which case, Id suggest a sample manifest format.
Hi! Everything is explained here https://docs.qiime2.org/2019.1/tutorials/importing/
type - you should indicate which type of reads you are going to use, for some of them you should also indicate input format
input path - path to your reads
output path - path to the place where you want to locate output files
The byte representing quality runs from 0x21 (lowest quality; '!' in ASCII) to 0x7e (highest quality; '~' in ASCII). Here are the quality value characters in left-to-right increasing order of quality (ASCII):
The original Sanger FASTQ files also allowed the sequence and quality strings to be wrapped (split over multiple lines), but this is generally discouraged as it can make parsing complicated due to the unfortunate choice of "@" and "+" as markers (these characters can also occur in the quality string).
Hello @Mehrdad - I have merged your two parallel discussion threads into one, please refrain from opening another thread with the same question, this takes up valuable time on our end, where we could be providing actual user support, rather than spending time on this kind of administration.
@Mehrdad - can you please provide the following: a screenshot of your raw files (we need to see the filenames)? Once we have a better idea of what shape your data currently is we can provide a more concrete recommendation. In the meantime, I think your most likely bet is to use the FASTQ Manifest format.