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Bismark Alignment very slow #670
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Increasing the the mismatches from the default (0) to |
Thanks for the quick reply. WARNING: Bismark Parallel (BP?) is resource hungry! Each value of --parallel specified With --parallel 4 it is taking ~40GB RAM. If we increase it to --parallel 8 or 10 it will take a lot of memory. I think this is difficult as it needs more RAM also. Also Is it recommended to use mismatches (0) ? |
This is from the Bowtie 2 manual:
Sets the number of mismatches to allowed in a seed alignment during multiseed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Default: 0. To be honest, I don't think I have ever changes this to 1 ever. It only really requires one multi-seed alignment in the read somewhere as anchor, which in my experience is pretty much always the case. |
Okay. Thanks for your response. Please suggest about : With --parallel 4 it is taking ~40GB RAM. If we increase it to --parallel 8 or 10 it will take a lot of memory. Is there any solution for this? |
I am afraid there isn't really a solution for this, if you ask for more memory it will also use more... You could potentially try to give each Bowtie2 thread some additional core (e.g.
|
Okay, so it means it will use 16 CPUs in total and ~40GB RAM? |
If you open a second terminal and run |
Hi Team,
I am running Bismark with the below command. I can see it's really slow.
bismark --bowtie2 -N 1 --parallel 4 $RESOURCES2/HG38/ -1 $Read1 -2 $Read2 --output_dir $PWD --temp_dir $PWD/$SAMPLEID"_TEMP" --prefix $SAMPLEID
I have 218,289,382 total reads i.e. 32.96(Gb) data. I did pre processing using Trimmomatic. Filtered reads are used for this.
It took ~22 h to complete. Can you please help with this?
Bismark Version: v0.24.0
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