Bug report of Oyster River Protocol made by macmanes lab.

[Sato Ryoma]

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

 

 

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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