/usr/bin/bash: seqtk: command not found

[Cory Bishop]

Hello, 

received this error:

/usr/bin/bash: seqtk: command not found

upon issuing this command from PacBio CCS SOP:

parallel -j 4 'seqtk seq -r {} > raw_data_rc/{/.}_rc.fastq' ::: raw_data/*.fastq

.fastq files get specified in raw_data_rc folder, but not populated with data. 

Attempted remedies: 

updated miniconda3 environment

updated QIIME2

installed latest version of seqtk based on instructions linked out from SOP. 

verified seqtk installed in 'pkgs' folder in miniconda3 environment

thoughts?

[Andre Comeau]

For the others on the group, Cory managed to find the solution to his problem:

"I figured out the issue on my end, pertinent to this morning's post by me. The instructions on the seqtk github page do not work for my linux system, so I had to issue a 'sudo apt install seqtk' command instead of 'make' as suggested."

FYI: We are soon going to update the PacBio Amplicon SOP to utilize the new -pacbio flag capacity on the latest DADA2 plugin for Q2 and so the use of seqtk might be deprecated in this new SOP.

	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, October 18, 2022 9:42 AM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: [microbiome-helper] /usr/bin/bash: seqtk: command not found

 

CAUTION: The Sender of this email is not from within Dalhousie.

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