User: Berghopper

gravatar for Berghopper
Berghopper20
Reputation:
20
Status:
New User
Location:
Kampen, Netherlands
Website:
http://ccpeters98.com/...
Last seen:
5 months, 1 week ago
Joined:
1 year, 9 months ago
Email:
c*****@hotmail.com

Posts by Berghopper

<prev • 12 results • page 1 of 2 • next >
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Answer: A: ReviGO down, any alternatives for GO enrichment condensing?
... Possibly EnrichR? http://amp.pharm.mssm.edu/Enrichr/ ...
written 5 months ago by Berghopper20
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Converting Ensembl stable ids to symbol, is version ID important for expression data?
... Dear Bioconductor, For my project I want to analyze a bunch of long non-coding RNA's (lncRNA) with TCGA (filters: transcriptome profiling, gene expression quantification, RNA-seq, FPKM) expression data of specific cancers. The resulting data for each gene uses versioned Ensembl ids and I need to c ...
lncrnas ensembl ids symbol conversion rna-seq written 5 months ago by Berghopper20
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Comment: C: snakemake on slurm cluster - jobs not updating/submitting after checkpoints? (Er
... Bump, It was actually not a mistake in the documentation... ...
written 6 months ago by Berghopper20
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Comment: C: snakemake on slurm cluster - jobs not updating/submitting after checkpoints? (Er
... Actually, it is still not solved sadly, I have contacted the slurm cluster admins and they state that I CAN use 400 jobs after all. So either this is a slurm bug or snakemake failing to handle this many jobs. Either way, as a workaround for now I'll probably make a separate intermediary script that ...
written 6 months ago by Berghopper20
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Answer: A: snakemake on slurm cluster - jobs not updating/submitting after checkpoints? (Er
... The reason this was happening was because of slurms job scheduler... Sadly, UiO's documentation listed that you can max utilize ~400 jobs. (https://web.archive.org/web/20190314224204/https://www.uio.no/english/services/it/research/hpc/abel/help/user-guide/queue-system.html#General_Job_Limitations) W ...
written 6 months ago by Berghopper20
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Comment: C: snakemake on slurm cluster - jobs not updating/submitting after checkpoints? (Er
... I think I resolved my issue, see my latest comment. ...
written 6 months ago by Berghopper20
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Comment: C: snakemake on slurm cluster - jobs not updating/submitting after checkpoints? (Er
... I don't know yet, I added this more as a safety feature for if the main "daemon" job terminates and the child jobs are still pending. I'll try remove it and report back. I also added another comment, you may be on the right track actually. ...
written 6 months ago by Berghopper20
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Answer: A: snakemake on slurm cluster - jobs not updating/submitting after checkpoints? (Er
... **Ok, update time:** What I've noticed is that, if I dial down the `-j` option (jobs submitted at the same time) the pipeline is a lot more stable for some reason. I don't know why this is, but I imagine this is more a bug/something regarding slurm rather than snakemake... ...
written 6 months ago by Berghopper20
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snakemake on slurm cluster - jobs not updating/submitting after checkpoints? (Error submitting jobscript (exit code 1):)
... Dear Biostars, I have a pretty complicated pipeline I need to run on a slurm cluster, but am not able to get it to work. For some reason, the pipeline works for smaller jobs, but as soon as I add more input files for more rigorous testing, it doesn't want to finish correctly. I don't have a minim ...
software error slurm snakemake written 6 months ago by Berghopper20
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Comment: C: LncRNA2Function unavailable - mirror?.
... We've tried this already, it's been tough so far. ...
written 11 months ago by Berghopper20

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Scholar 6 months ago, created an answer that has been accepted. For A: snakemake on slurm cluster - jobs not updating/submitting after checkpoints? (Er

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