Comments (14)
Yes. Now it's good! Thanks!
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@zhangb1 do you have an eta for this ticket?
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@jharenza can someone from your team take care of the ticket, maybe run?
I really need to focus on the data assembly cwl develop this week.
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I don't think she has ec2 access yet and we have a lot of open issues for OT that need to be done as well - @yuankunzhu can someone else help with these upstream processes?
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Trying to run locally but have the memory issue. can't process
I need to wrap the cwl and try to run on cavatica project.
the error
➜ GTEx Rscript 00-collapse_matrices.R -i gene-expression-rsem-tpm.rds -g gencode.v27.primary_assembly.annotation.gtf.gz -m gene-expression-rsem-tpm-collapsed.rds -t gene-expression-rsem-tpm-collapsed_table.rds -n GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
[1] "Generating input matrix and drops table...!"
[1] "Read merged GTEx data"
── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
cols(
.default = col_double(),
Name = col_character(),
Description = col_character()
)
ℹ Use `spec()` for the full column specifications.
[1] 95949 killed Rscript 00-collapse_matrices.R -i gene-expression-rsem-tpm.rds -g -m -t -n
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I had to run it on a large EC2, GTEx files are huge
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I ran the gtex collapsed data on cavatica project
here: https://cavatica.sbgenomics.com/u/zhangb1/test-download/tasks/2d842fee-65cf-4c5b-b1aa-0e458b2dfa29/
and I ran the pbta-gmkf-gene-expression-rsem-tpm-collapsed.rds
locally.
when I tried to merge the files using the notebook.
> common_genes <- intersect(rownames(gtex),rownames(pbta_gmkf))
> length(common_genes)
[1] 0
the length of the common_genes is 0.
@kgaonkar6 can you take a look?
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wait. I think I found the issue. l will check
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the merged files has been updated in the bucket:
2021-07-21 14:54:03 1073668357 gene-counts-rsem-expected_count-collapsed.rds
2021-07-21 14:28:30 1611312452 gene-expression-rsem-tpm-collapsed.rds
md5 also updated
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Thanks a lot @zhangb1 !!
@runjin326 can you try to download these files with the updated download-data.sh pointing to v7 s3 bucket? Since you need for fusion_filteering rerun?
from d3b-bixu-data-assembly.
@kgaonkar6, @zhangb1, thanks so much! Yes I have downloaded the data and should be able to re-run fusion_filtering now.
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Oh sorry forget to mention, @kgaonkar6 - the md5sum did not match. I am guessing that is because they are updated?
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Could you removegene-counts-rsem-expected_count-collapsed.rds
and gene-expression-rsem-tpm-collapsed.rds
in your local data
folder and rerun download-data.sh
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Closing this as we have this data available in OT.
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