Error in rule make_gene_quant_dataframe_ref #237
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The rule that failed involves a custom script to gather the results of quantification. Could you please attach |
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Yes of course, below is the content? |
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Do you still have the files I think this may fix the error, but if the files are empty, I'm not sure that pipeline will yield much, and there may be more issues downstream. #238 |
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They do have about 60K lines not sure what are those extra 2 lines in R2 though? |
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That is strange! They seem pretty similar, though, and might be usable. I'd suggest running the other workflows (variant & isoform) to let them finish, and then work on analysis using those two quantification files. Please let me know if you figure out what the difference is if you figure it out. I have very limited time for this project, so I'll leave it there for now. If it makes your downstream analysis impossible, I'd be happy to try to help some more. |
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is there some documentation to follow so that i can run this all on a linux cluster without docker but singularity? |
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Hi @animesh, Spritz doesn't have singularity capabilities yet. That'd be a welcome pull request if you know how to do it. The way I've run it on the cluster is just to use Snakemake without containers, for which you can find instructions here, https://github.com/smith-chem-wisc/Spritz/wiki/Spritz-commandline-usage#spritz-commandline-usage. |
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Hi, i am having a similar issue when running Spritz from the command line. I see that there is a branch and pull request for a fix at #238 and i was wondering if this can be used as a fix because it has not yet been merged to main. |
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I merged it and made a new release. Let's see if that fixes the issue. 👍🏼 |
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Well, that didn't work. I'll get the release working by the end of the day and update you. |
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The new release is available now. (The issues were just version checking.) |
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Thank you so much! I will try this tomorrow in the morning and let you know :) I also didn't mean to make you do the merge, i was just wondering if i can checkout that branch and use the fix or if something on that branch was still missing. But this is even better |
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Did the fix work for you? |
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Hey, sorry for taking so long to get back to you. We had some other stuff coming up in the lab and i didn't have time to check any further... Unfortunately it didn't fix the issue, but it might be an error on our side since we have a bit of trouble with the computer that we are testing this on. I will let you know if i make any progress on this. Sorry for leaving you hanging for so long. |
I am trying to use the beta functions
but facing this error (log below), any ideas how to proceed?
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