Hi, I submitted three datasets to the MethylDackel tool and it is running for the past two days (other users said it took them 2-3 hours to get results). does anyone know what’s the problem? Thanks

Any reason you can not use … [grafik]

Hi @Guy_Haim , I have this here in your logs. [fai_load] build FASTA index. [fai_load] build FASTA index. [fai_load] build FASTA index. [fai_load] build FASTA index. [fai_load] build FASTA index. [fai_load] build FASTA index. [fai_load] build FASTA index. [fai_load] build FASTA index. [fai_load] bu…

Yes, my own index. 13: GRCh38.primary_assembly.genome.fa uncompressed do you think I should use another index?

not that I can think of (except I used it for the previous stages of the reduced representation bisulfite sequencing files I got). anyway, I’ll try…

Please let me know if this speeds up your processing.

Hi again, it’s still running. How long does it take normally? Also, do you think I should re-do the previous stages? This time with this ref genome: [image]

Hi @Guy_Haim Using the same exact reference genome (build + version) throughout analysis is important. The natively indexed version of hg38 was sourced from UCSC . If that is the same as what you used for upstream steps (in Galaxy or not), all should be fine. Other reference genome sources can be …

Hi, thanks for replying… Actually, I was told to use the built-in genome index in galaxy instead of the index I created on my own, but it didn’t work and I used it for the upstream steps and for the MethylDackel tool as well. Still, it’s running for almost two weeks now. If you can think of anyth…

@Guy_Haim Using mammalian or some plant genomes, that are large, tends to exceed resources at public Galaxy servers when input as a custom genome (fasta) from the history. Why? Because before the tool is run, the genome may need indexing. I saw that you are now using the built-in index, so that wil…

OK, I’ll try… Thank you so much for the help. Guy בתאריך יום ו׳, 4 ביוני 2021, 22:34, מאת Jennifer Hillman-Jackson via Galaxy Community Help ‏< galaxy@discoursemail.com >:

Galaxy Community Help

MethylDackel running time too long

usegalaxy.eu support

custom-genome, queued-gray-datasets

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