Maria Virginia Ruiz Cuevas
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Latest activity by Maria Virginia Ruiz Cuevas
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Maria Virginia Ruiz Cuevas commented,
Hi Samatha, I have already run that command so I could use Samtools to read the BAM file. However, as shown in the screenshot below, the same issue persists even after re-running the authenticatio...
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Maria Virginia Ruiz Cuevas commented,
Hi Samantha, Thank you for your answer. I want to confirm that I am logged into the Google Cloud SDK. I have attached a screenshot showing that I can access the BAM file using samtools. However, w...
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Maria Virginia Ruiz Cuevas created a post,
Download GTEx bam files
Good afternoon, I am reaching as I have issues to download some GTEx bam files. For context, I have the necessary permissions for my NIH account and NHGRI AnVIL Data Commons on Terra. I can succes...
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Maria Virginia Ruiz Cuevas commented,
Hi Samantha (she/her)I wanted to know if you have any news regarding the last post about the connection closure. Thanks! MaVi
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Maria Virginia Ruiz Cuevas commented,
Hi Julia Kodysh Thanks for your reply! I just want to be sure that I understood correctly your message. Did you encounter the same problem (SSL cert) with pysam 0.22.0? Or any of the other problem...
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Maria Virginia Ruiz Cuevas commented,
Hi Samantha, Yes, indeed. Below I share the details of this workspace, I am sorry for the confusion. Here the other information:1. https://app.terra.bio/#workspaces/broad-firecloud-cptac/BamQuery2...
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Maria Virginia Ruiz Cuevas commented,
Hi Samantha, Sure, here is the submission ID: 09feba12-4fd3-43a4-a3da-92ba1210c22b You can see that in the last task that was executed call-module_2_counting_and_normalization/ Shard 2 got the mes...
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Maria Virginia Ruiz Cuevas commented,
Hi Samantha, I hope you had great holidays! I came back to this post as I still facing the same problem. I tried the max_retrites, however the same error appears. So I was wondering if my problem ...
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Maria Virginia Ruiz Cuevas commented,
Hi Samantha, I wanted to tell you that I managed to create a new docker that integrates samtools and pysam. Now I can do queries with both to bam files in the google bucket without locating them. ...
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Maria Virginia Ruiz Cuevas commented,
Hi Samantha, Thank you for taking the time to investigate this issue. Outside Terra, yes! Pysam is able to access the file. (base) -bash:login02:/prot/proteomics/LabMembers/MaVi/Projects/CLL/BamQ...
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