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macmanes-lab / Oyster_River_Protocol

Official Repository of the Oyster River Protocol for Transcriptome Assembly
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ORP 2.3.3 with docker doesn't start #48

Open marco91sol opened 2 years ago

marco91sol commented 2 years ago

I launch the following command: /home/orp/Oyster_River_Protocol/oyster.mk main STRAND=RF TPM_FILT=1 MEM=400 CPU=64 READ1=concatenated_R1.normalized.trimmed.fq R2=concatenated_R2.normalized.trimmed.fq RUNOUT=assembly --debug

It doesnt start and with --debug option, it gives me the following output: File 'main' does not exist. File 'setup' does not exist. File '/ORP_wd/assemblies/working' does not exist. Must remake target '/ORP_wd/assemblies/working'. Successfully remade target file '/ORP_wd/assemblies/working'. Must remake target 'setup'. Successfully remade target file 'setup'. File 'check' does not exist. Must remake target 'check'. Successfully remade target file 'check'. File 'welcome' does not exist. Must remake target 'welcome'.

What's the solution to this issue?

macmanes commented 2 years ago

Try taking out the main part and I think you should be all set. I’ll have to update the documentation.

Thanks, Matt

Matthew MacManes, RN, Ph.D. (he/him) University of New Hampshire Associate Professor of Genome Enabled Biology Faculty Senate Vice Chair Genetics Undergraduate Program Coordinator MCBS Graduate Program Facilitator Department of Molecular, Cellular, & Biomedical Sciences Durham, NH 03824 Phone: 603-862-4052 | Web: genomebio.orghttp://genomebio.org Office: 434 Gregg Hall | Laboratory: 437 Gregg Hall

UNH is located on the traditional lands of the Abenaki, Pennacook, and Wabanaki Peoples past and present. We acknowledge and honor with gratitude the land itself and the people who have stewarded it throughout the generations. We also acknowledge the hardships they continue to endure after the loss of unceded homelands and champion the university’s responsibility to foster relationships and opportunities that strengthen the well-being of the Indigenous People who carry forward the traditions of their ancestors.

From: marco91sol @.> Date: Monday, November 15, 2021 at 05:51 To: macmanes-lab/Oyster_River_Protocol @.> Cc: Subscribed @.***> Subject: [macmanes-lab/Oyster_River_Protocol] ORP 2.3.3 with docker doesn't start (Issue #48) CAUTION: This email originated from outside of the University System. Do not click links or open attachments unless you recognize the sender and know the content is safe.

I launch the following command: /home/orp/Oyster_River_Protocol/oyster.mk main STRAND=RF TPM_FILT=1 MEM=400 CPU=64 READ1=concatenated_R1.normalized.trimmed.fq R2=concatenated_R2.normalized.trimmed.fq RUNOUT=assembly --debug

It doesnt start and with --debug option, it gives me the following output: File 'main' does not exist. File 'setup' does not exist. File '/ORP_wd/assemblies/working' does not exist. Must remake target '/ORP_wd/assemblies/working'. Successfully remade target file '/ORP_wd/assemblies/working'. Must remake target 'setup'. Successfully remade target file 'setup'. File 'check' does not exist. Must remake target 'check'. Successfully remade target file 'check'. File 'welcome' does not exist. Must remake target 'welcome'.

What's the solution to this issue?

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