Hello. I started to learn microbiome analysis. For practice, I'd like to analysis 16S sequence data uploaded on database. This sequence data was obtained by pyrosequencing using 454 GS FLX Titanium (V1-V2 region). This have been already trimmed by quality, primer sequence, and 3000 reads were ran…

Hello @kopelol , This is a very broad question. What is your end goal when analyzing this data? If you are just trying to learn how analysis in QIIME 2 works in general, then I would suggest you do some of our tutorials starting with moving pictures if you haven't already.

Should I download R 4.2.0 or newer?

Hello @Oddant1 Thank you for your reply. I tried to perform analyze using following command. import qiime tools import \ --type SampleData[SequencesWithQuality] \ --input-path manufest.txt \ --output-path saliva.qza \ --input-format SingleEndFastqManifestPhred33 It seemed that this was …

Can you please copy paste the contents of that log file here? Thank you. In addition, what version of QIIME 2 are you using, and what compute environment are you using?

I'm using q2cli version 2024.5.0 with linux server environment. Here is the log. Traceback (most recent call last): File "/home/user/miniconda3/envs/qiime2-amplicon-2024.5-2/lib/python3.9/site-packages/q2cli/commands.py", line 520, in call results = self._execute_action( File "/home/user/minico…

Running external command line application(s). This may print messages to stdout and/or stderr. The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist. Command: run_dada.R --input_directory /tmp/qiime2/user/data/48471…

@kopelol This appears to be an issue we have seen before where there is an R installation outside of your conda environment that is being used inside of your conda environment in place of the one that ships with QIIME 2. With your conda environment active, can you please run the command which R and…

Thank you. It might be because of my server problems. Recently OS was updated, so I couldn't R. I tried to fi this problem. Best regards,

Sorry. I think problem about R has been solved, but another error was occured. This is the log. Running external command line application(s). This may print messages to stdout and/or stderr. The command(s) being run are below. These commands cannot be manually re-run as they will depend on tempo…

Hello. I'd like to analyse 454 sequene data downloaded from SRA. My question is Are the quality scores of 454 reads interpreted differently from those of other sequencing platforms? According to the paper, the data has been filtered based on quality values, but the FASTQ file still contains re…

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