Hello Team,
I am starting my research of Master in Environmental Science and Technology. I need to carry out analysis of readings made available in the NCBI. I’m trying to make the prediction through PiCrust. I looked for several tutorials on this subject. I have not found any tutotial that analyzes the 16s Illumina files from NCBI, these files are in fastaq format, unique file. Can you help me?
Hello Engo! Welcome to the Qiime 2!
As you have already looks for tutorials, you have probably found this tutorial about running Picrust in Qiime 2: q2 picrust2 Tutorial · picrust/picrust2 Wiki · GitHub
You can import the fastq files you received from NCBI using the fastq-manifest-format.
Let us know if you have any questions,
Colin
P.S. And if this is your first time using Qiime 2, check out this excellent tutorial:
https://docs.qiime2.org/2019.1/tutorials/moving-pictures/
Thanks Colinbrislawn !
i´ll try!
Hi Colinbrislawm,
I tried to do as you passed me, but I’m having this error:
(qiime2-2019.1) [rafael@bioinfo2 testeqiimedir]$ qiime tools import --type ‘SampleData[SequencesWithQuality]’ --input-path ManifestFile --output-path single-end-demux.qza --input-format SingleEndFastqManifestPhred64V2
/bin/sh: Symbol `rl_readline_state’ has different size in shared object, consider re-linking
Traceback (most recent call last):
*** File “/home/rafael/dados/Miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/util.py”, line 91, in parse_format***
*** format_record = pm.formats[format_str]***
KeyError: 'SingleEndFastqManifestPhred64V2’
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
*** File “/home/rafael/dados/Miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/tools.py”, line 146, in import_data***
*** view_type=input_format)***
*** File “/home/rafael/dados/Miniconda/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/rafael/dados/Miniconda/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: SingleEndFastqManifestPhred64V2
An unexpected error has occurred:
*** No format: SingleEndFastqManifestPhred64V2***
See above for debug info.
I downloaded my files from NCBI and extracted the FASTQ through the NCBI toolkit.
link to my .sra
https://www.ncbi.nlm.nih.gov/sra/SRX3151516[accn]
Can u help me ?
The issue is that you have QIIME 2 version 2019.1 installed, but are following the instructions for version 2019.4 (in which new manifest formats have been introduced and are used in the tutorial).
You have two choices:
- Follow the 2019.1 documentation (the link @colinbrislawn provided above will direct you to the older documentation)
- install the latest version of QIIME 2 and use the latest documentation (what you used in your command)
Good luck!
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