User: Berghopper

gravatar for Berghopper
Berghopper10
Reputation:
10
Status:
New User
Location:
Kampen, Netherlands
Website:
http://ccpeters98.com/...
Last seen:
1 day, 6 hours ago
Joined:
1 year, 3 months ago
Email:
c*****@hotmail.com

Posts by Berghopper

<prev • 10 results • page 1 of 1 • next >
0
votes
2
answers
111
views
2
answers
Comment: C: snakemake on slurm cluster - jobs not updating/submitting after checkpoints? (Er
... Bump, It was actually not a mistake in the documentation... ...
written 1 day ago by Berghopper10
0
votes
2
answers
111
views
2
answers
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 1 day ago by Berghopper10
0
votes
2
answers
111
views
2
answers
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 7 days ago by Berghopper10
0
votes
2
answers
111
views
2
answers
Comment: C: snakemake on slurm cluster - jobs not updating/submitting after checkpoints? (Er
... I think I resolved my issue, see my latest comment. ...
written 7 days ago by Berghopper10
0
votes
2
answers
111
views
2
answers
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 7 days ago by Berghopper10
0
votes
2
answers
111
views
2
answers
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 7 days ago by Berghopper10
1
vote
2
answers
111
views
2
answers
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 7 days ago by Berghopper10
0
votes
0
answers
220
views
0
answers
Comment: C: LncRNA2Function unavailable - mirror?.
... We've tried this already, it's been tough so far. ...
written 5 months ago by Berghopper10
0
votes
0
answers
220
views
0
answers
LncRNA2Function unavailable - mirror?.
... So I am a bachelor student doing an internship. Right now I am developing an R package. I cannot tell much more about this because it is slightly confidential. I however wanted to ask about the lncRNA2Funcion data. It seems to have been offline for quite some time now. I can however say that I WIL ...
lncrna2function lncrna rna-seq data written 5 months ago by Berghopper10
0
votes
1
answer
468
views
1
answer
Trying to make metaphlan2 work with krona for school project; need fastq files to test with.
... referably I would need old and new versions of the fastq format for both paired and single-ended data. I already searched ncbi but is a pain to find anything remotely useful. Does anybody have a few files that they know will work and give a comprehensible result with metaphlan2? It does not need to ...
krona metagenomics examples metaphlan2 fastq written 15 months ago by Berghopper10 • updated 15 months ago by h.mon24k

Latest awards to Berghopper


Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2204 users visited in the last hour