> 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....@gnu.org> on behalf of Sato Ryoma <sato.ryoma....@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....@s.kyushu-u.ac.jp
