I am trying to access the files from MNT/PROJECT but not accessible

03 February 2023 00:00
4 comments

Hello,

I am trying to use data in /mnt/project and upload it to hail and do the subsequent analysis. Although the results are running well when I did the initial import_plink. I am getting a file not found error, I also tried copying to opt/notebooks folder and tried again still could able to access the files. I thought its a permissions error so I changed the permissions. I tried to upload the files to hail. It worked while uploading but when I am counting the number of individuals. I am getting a file not found error. Please do let me know how to resolve this.

I also tried the hail-in-DNAnexus package generated to use the latest version of hail but was unsuccessful in it.

I have checked the ls command on the mnt/project folder and I could able to see and access the files not sure what's going wrong.

Please do let me know a workaround for this.

I have also made sure the files are present in the mnt./ project before initiating the cluster.

Regards

Akhil

Comments

4 comments

Alexandra Lee DNAnexus Team
- 03 February 2023 20:10
Hi Akhil,

Would you mind providing some screenshots to further clarify what you're doing/what issue you're running into. Thanks

0
Former User of DNAx Community_6
- 06 February 2023 16:18
Hello Alexandra, Thank you for the response. I am getting this error when i am trying to upload files to hail using mnt/project filesystem

``` Code
ukbb1 = hl.import_plink(bed="file:///mnt/project/Bulk/'Genotype Results'/'Genotype calls'/ukb22418_c1_b0_v2.bed",bim="file:///mnt/project/Bulk/'Genotype Results'/'Genotype calls'/ukb22418_c1_b0_v2.bim",fam="file:///mnt/project/Bulk/'Genotype Results'/'Genotype calls'/ukb22418_c1_b0_v2.fam",reference_genome='GRCh37')```

Error:

Even though the files are in the folder

Let me know if this helps.

Regards
Akhil

0
Alexandra Lee DNAnexus Team
- 06 February 2023 17:21
Hi Akhil,

Thanks for sharing this, it looks like its how you're defining your file path names using strings in the python notebook, which is different than bash.

Hope this helps

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Former User of DNAx Community_6
- 06 February 2023 17:46
Got it. Thank you so much. I used to have problems while uploading from a folder based on spaces in the naming convention so used the quotes. I am checking the error right now and it looks like it's working fine. Thank you so much for the update.

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