1.7 Import FASTQs as QIIME 2 artifact

[Cory Bishop]

Trying to import PACBIO reads as .qza artifact with this command from PacBio CCS Amplicon SOP v1. I have completed prior trimming steps.

qiime tools import \

--type SampleData[SequencesWithQuality] \

--input-path PacBioCCSmanifest.tsv \

--output-path reads_qza/trimmed_reads.qza \

--input-format SingleEndFastqManifestPhred33V2

generates the following error:

"Importing 'SingleLanePerSampleSingleEndFastqDirFmt' requires a directory, not PacBioCCSmanifest.tsv"

I am issuing this command from the same directory in which the .tsv file is located and would not think  an explicit directory path is required. Indeed when I provided one, it did not solve the problem. What am I missing?

thanks

Cory

[Andre Comeau]

Cory,

This should work as it did in my testing, but what version of QIIME2 are you using? It could be a slight change in the import options wording since an update.

	ANDRÉ M. COMEAU, PhD Manager • Integrated Microbiome Resource (IMR) T: 902.494.2684 | E: andre....@dal.ca	​Address for deliveries: Dept. of Pharmacology Tupper Med. Bldg., room 5D Dalhousie University 5850 College St. Halifax NS B3H 4R2
​	Research Associate (Lab Manager) Morgan Langille Lab • Dept. of Pharmacology ResearchGate Profile • GoogleScholar Publications
"Without fantasy, there is no science. Without fact, there is no art." - Nabokov "The good thing about science is that it's true whether or not you believe in it." - Neil deGrasse Tyson

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From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of Cory Bishop <symbio...@gmail.com>
Sent: Tuesday, August 24, 2021 1:03 PM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: [microbiome-helper] 1.7 Import FASTQs as QIIME 2 artifact

 

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[Andre Comeau]

PS: Does your manifest file look like this (for example)?

# single-end PHRED 33 fastq manifest file for forward reads

sample-id       absolute-filepath

CLO_A_P1_05     $PWD/trimmed_reads/CLO_A_P1_05_cat_trim.fastq

CLO_A_P1_09     $PWD/trimmed_reads/CLO_A_P1_09_cat_trim.fastq

Note that you might have the PWD as your absolute location written out instead (ex: /home/cory/project_name/...).

	ANDRÉ M. COMEAU, PhD Manager • Integrated Microbiome Resource (IMR) T: 902.494.2684 | E: andre....@dal.ca	​Address for deliveries: Dept. of Pharmacology Tupper Med. Bldg., room 5D Dalhousie University 5850 College St. Halifax NS B3H 4R2
​	Research Associate (Lab Manager) Morgan Langille Lab • Dept. of Pharmacology ResearchGate Profile • GoogleScholar Publications
"Without fantasy, there is no science. Without fact, there is no art." - Nabokov "The good thing about science is that it's true whether or not you believe in it." - Neil deGrasse Tyson

---

From: Andre Comeau <Andre....@Dal.Ca>
Sent: Tuesday, August 24, 2021 1:14 PM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: Re: [microbiome-helper] 1.7 Import FASTQs as QIIME 2 artifact

 

[Cory Bishop]

yep, that could be it, I am using 2018.6. I'll update and then post if it worked upon update

C

[Andre Comeau]

OK - I tested on 2019.7 and so is working at least on that version (if not later ones).

	ANDRÉ M. COMEAU, PhD Manager • Integrated Microbiome Resource (IMR) T: 902.494.2684 | E: andre....@dal.ca	​Address for deliveries: Dept. of Pharmacology Tupper Med. Bldg., room 5D Dalhousie University 5850 College St. Halifax NS B3H 4R2
​	Research Associate (Lab Manager) Morgan Langille Lab • Dept. of Pharmacology ResearchGate Profile • GoogleScholar Publications
"Without fantasy, there is no science. Without fact, there is no art." - Nabokov "The good thing about science is that it's true whether or not you believe in it." - Neil deGrasse Tyson

From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of Cory Bishop <symbio...@gmail.com>

Sent: Tuesday, August 24, 2021 1:21 PM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: Re: [microbiome-helper] 1.7 Import FASTQs as QIIME 2 artifact

 

To view this discussion on the web visit https://groups.google.com/d/msgid/microbiome-helper/ec712d59-8cdf-4677-b4b8-d4fb36f65102n%40googlegroups.com.