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course-fish546-2023 / assistance-public

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Issues converting SAM to BAM #14

Open scuba-sarah opened 1 year ago

scuba-sarah commented 1 year ago

See screenshot. I'm assuming this is not what I want?

Screenshot 2023-05-05 145413

sr320 commented 1 year ago

try changing sam to /home/shared/8TB_HDD_01/sr320/github/steven-crabby-duck/output/F143_cgigas.sam

scuba-sarah commented 1 year ago

Nah, I got the same issue.

sr320 commented 1 year ago

url for Rmd file and line #?

scuba-sarah commented 1 year ago

Sorry, I just pushed. https://github.com/course-fish546-2023/sarahyerrace-coursework/blob/main/assignments/code/06_Alignment_Data.Rmd line 116

sr320 commented 1 year ago

I just ran - no issues

see https://d.pr/i/orVouR

scuba-sarah commented 1 year ago

yeah it'll run for a while then stop for me. And then the next chunk won't run either

sr320 commented 1 year ago

running code in your repo.... https://d.pr/i/EfsZQ1 no errors. Are you running on raven?

scuba-sarah commented 1 year ago

Yes