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Re: Bug report of Oyster River Protocol made by macmanes lab.


From: Martin Dorey
Subject: Re: Bug report of Oyster River Protocol made by macmanes lab.
Date: Tue, 11 Jan 2022 02:05:02 +0000

> I found a bug

If you have, then it's more likely in the documentation for this "Oyster River Project" than in the code of the Oyster River Project itself, let alone Gnu Make.

> /bin/bash: activate: No such file or directory

That looks like the kind of problem you get when one of Python's "virtualenv" things hasn't been activated.  One of Google's first matches for Oyster River Project is https://github.com/macmanes-lab/Oyster_River_Protocol, which points to https://hackmd.io/@macmanes/SJhOQvkVm?type=view# which suggests that you might need to "Launch the conda environment" first.  I won't be surprised if that doesn't help, because I'm afraid, Sato-san, you've come to the wrong place.  No one here is likely to know anything about the Oyster River Project.  I'm afraid it wasn't clear to me in a few minutes of googling where the right place might be.  Good luck.


From: Bug-make <bug-make-bounces+martin.dorey=hds.com@gnu.org> on behalf of Sato Ryoma <sato.ryoma.743@s.kyushu-u.ac.jp>
Sent: Monday, January 10, 2022 15:53
To: bug-make@gnu.org <bug-make@gnu.org>
Subject: Bug report of Oyster River Protocol made by macmanes lab.
 
***** EXTERNAL EMAIL *****

Hello, my name is Ryoma Sato.

I am a second-year master's student at the Graduate School of Bioresources and Environmental Sciences, Kyushu University in Japan.

 

I have started the Oyster River Protocol, but I found a bug, so I will send you a report.

Please check the following information. I would like you to tell me where is wrong.

We are sorry for any inconvenience this may cause you, but we appreciate your cooperation.

 

(orp_v2) [iceplant4561@at137 sampledata]$ ~/Oyster_River_Protocol/oyster.mk main STRAND=RF MEM=15 CPU=8 READ1=test.1.fq.gz READ2=test.2.fq.gz RUNOUT=test

/bin/bash: activate: No such file or directory

SALMON installed

/bin/bash: activate: No such file or directory

/bin/bash: activate: No such file or directory

/bin/bash: activate: No such file or directory

BUSCO installed

/bin/bash: activate: No such file or directory

/bin/bash: activate: No such file or directory

SPADES installed

/bin/bash: activate: No such file or directory

TRINITY installed

/bin/bash: activate: No such file or directory

TRIMMOMATIC installed

/bin/bash: activate: No such file or directory

TRANSABYSS installed

/bin/bash: activate: No such file or directory

RCORRECTOR installed

 

 

*****  Welcome to the Oyster River *****

*****  This is version 2.3.3 *****

 

 

 

/bin/bash: activate: No such file or directory

ERROR, don't recognize parameter: --no_normalize_reads

Please review usage info for accepted parameters.

make: *** [/lustre7/home/iceplant4561/Oyster_River_Protocol/sampledata/assemblies/test.trinity.Trinity.fasta] Error 255

 

 

---------------------------

Kyushu University Graduate School

Graduate School of Bioresource and Environmental Sciences

Course of Agricultural Bioscience, Department of Bioresource Sciences

Plant Production Physiology Laboratory, 2nd year master's student

Ryoma Sato

Mail: sato.ryoma.743@s.kyushu-u.ac.jp

 


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