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Permissions issue with kallisto #20

Open cskalley opened 1 year ago

cskalley commented 1 year ago

I get a "permission denied" error when I try to run kallisto with the opilio transcriptome. I tried re-running kallisto on the bairdi transcriptome that I had gotten to work before but am getting an error for that too, so I think it might be an issue with kallisto?

Starts on line 70:

https://github.com/course-fish546-2023/courtney_RNAseq_crabs/blob/58ba0ec5df6e9457b88a458a1a7f096509cad1e6/code/snowcrabs.Rmd

sr320 commented 1 year ago

It’s likely not kallisto- post the exact code you are trying to run, and the exact entire error message

On Thu, May 25, 2023 at 7:15 PM Courtney Skalley @.***> wrote:

I get a "permission denied" error when I try to run kallisto with the opilio transcriptome. I tried re-running kallisto on the bairdi transcriptome that I had gotten to work before but am getting an error for that too, so I think it might be an issue with kallisto?

Starts on line 70:

https://github.com/course-fish546-2023/courtney_RNAseq_crabs/blob/58ba0ec5df6e9457b88a458a1a7f096509cad1e6/code/snowcrabs.Rmd https://urldefense.com/v3/__https://github.com/course-fish546-2023/courtney_RNAseq_crabs/blob/58ba0ec5df6e9457b88a458a1a7f096509cad1e6/code/snowcrabs.Rmd__;!!K-Hz7m0Vt54!hn-SaSA3xfdLyFnO5iI-LlV4xEDt9hOmZr_U8xyCfUJ7LsRMBkDmmnrfQAe1lBp3PXF87BLHCcrqbz4bo5lMRVk$

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Steven B. Roberts, Professor Associate Director - Graduate Program Coordinator School of Aquatic and Fishery Sciences University of Washington Fisheries Teaching and Research (FTR) Building - Office 232 1140 NE Boat Street - Seattle, WA 98105 robertslab.info - @.*** - @sr320 vm:206.866.5141 - cell:360.362.3626 schedule a zoom call: https://d.pr/gsgxVJ

cskalley commented 1 year ago 
/home/shared/kallisto/kallisto \
index -i \
../data/c_opilio_mg_transcriptome.index \  
../data/c_opilio_mg_transcriptome.fasta

Error: FASTA file not found
/tmp/RtmpFAsogu/chunk-code-b22211646340.txt: line 4: ../data/c_opilio_mg_transcriptome.fasta: Permission denied

It's probably that I'm making a mistake somewhere, but the .fasta file is in /data and the name matches. I've also used that .fasta file for blast so it's definitely there...

sr320 commented 1 year ago

The backslash after index…. I believe there are spaces after the backslash- make sure to delete those

On Thu, May 25, 2023 at 7:41 PM Courtney Skalley @.***> wrote:

/home/shared/kallisto/kallisto \ index -i \ ../data/c_opilio_mg_transcriptome.index \ ../data/c_opilio_mg_transcriptome.fasta

Error: FASTA file not found /tmp/RtmpFAsogu/chunk-code-b22211646340.txt: line 4: ../data/c_opilio_mg_transcriptome.fasta: Permission denied

It's probably that I'm making a mistake somewhere, but the .fasta file is in /data and the name matches. I've also used that .fasta file for blast so it's definitely there...

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/course-fish546-2023/assistance-public/issues/20*issuecomment-1563634602__;Iw!!K-Hz7m0Vt54!gs8SppvsYjKtxHbyMk_SNmwS_PF6XTBLRgB_PBXsX0jjV7CqikL84H4aETYafWXbGJQY4uEdDRyER30BtV5V5O8$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABB4PN3OLV3JUJC5I5ORE23XH7UY5ANCNFSM6AAAAAAYPPQYPI__;!!K-Hz7m0Vt54!gs8SppvsYjKtxHbyMk_SNmwS_PF6XTBLRgB_PBXsX0jjV7CqikL84H4aETYafWXbGJQY4uEdDRyER30BQ1LfimM$ . You are receiving this because you were mentioned.Message ID: @.***>

--

Steven B. Roberts, Professor Associate Director - Graduate Program Coordinator School of Aquatic and Fishery Sciences University of Washington Fisheries Teaching and Research (FTR) Building - Office 232 1140 NE Boat Street - Seattle, WA 98105 robertslab.info - @.*** - @sr320 vm:206.866.5141 - cell:360.362.3626 schedule a zoom call: https://d.pr/gsgxVJ

sr320 commented 1 year ago

Just confirmed that was issue. I was able to make index.. If it makes you feel different the backslash was red on my screen indicating some type of issue :) https://d.pr/i/qZADCy

cskalley commented 1 year ago

I don't know if I should feel frustrated or relieved. I'll remember to check for that one of these days...

On Thu, May 25, 2023 at 5:19 PM Steven Roberts @.***> wrote:

Just confirmed that was issue. I was able to make index.. If it makes you feel different the backslash was red on my screen indicating some type of issue :) https://d.pr/i/qZADCy https://urldefense.com/v3/__https://d.pr/i/qZADCy__;!!K-Hz7m0Vt54!neUqbVGrSQKYKULfSkUZ_uBFAye_RAerxrpcu1r4jdI1WjbhxfBTCYtrAffjoJF8kVukCNewUAH0XZz4EsevoO2K$

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