User: little_more

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little_more10
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Posts by little_more

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Comment: C: bwa parallel on a SLURM cluster
... I see. Thanks very much for your help! ...
written 6 weeks ago by little_more10
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Comment: C: bwa parallel on a SLURM cluster
... I see. so every task will run on a separate CPU and a node needs to have 34 CPUs? ...
written 6 weeks ago by little_more10
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Comment: C: bwa parallel on a SLURM cluster
... so you suggest using: #SBATCH --nodes=1 #SBATCH --ntasks-per-node=8 parallel -j 2... right? sorry for many questions I just started working with this cluster and I was surprised when `parallel -j ` ran longer than just `parallel` ...
written 6 weeks ago by little_more10
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Comment: C: bwa parallel on a SLURM cluster
... [ATpoint][1], thanks for answering to *my* question without endless referring to snakemake! :) clusters specifications: 376 nodes: each with 2 processors (8 cores each) & 64 GB RAM 144 nodes: each with 2 processors (12 cores each) & 64 GB RAM do you specify how much memory you need wit ...
written 6 weeks ago by little_more10
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bwa parallel on a SLURM cluster
... I'm working on a SLURM cluster with NGS data. I trimmed raw reads and was thinking of the best way to align them to the reference genome. I have pairs of reads for a few samples. I wrote a script for parallel bwa: #SBATCH --cpus-per-task=1 #SBATCH --ntasks=10 #SBATCH --nodes=1 # al ...
bwa written 6 weeks ago by little_more10
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Comment: C: bwa mem: fail to locate the index files
... it works now, thank you very much! ...
written 7 weeks ago by little_more10
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bwa mem: fail to locate the index files
... Hi all, I have a problem with running bwa in parallel. I'm using this script (as kindly suggested in [this topic][1]): # reference hg1kv37=/dir/to/reference/and/index/files/human_g1k_v37.fasta # create a function bwatosam() { id="$1" bwa mem -t 10 -R "@RG\tID ...
bwa written 7 weeks ago by little_more10 • updated 7 weeks ago by ole.tange3.5k
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Comment: C: using GNU parallel for bwa mem and samtools
... I seem to overcome the problem with bwa: I just added a path to `~/.bashrc` file. Now I have another issue: [E::bwa_idx_load_from_disk] fail to locate the index files although the dir contains index files. What should I do? ...
written 7 weeks ago by little_more10
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Comment: C: using GNU parallel for bwa mem and samtools
... thank you all for your answers! @h.mon, I tried various combinations of quotes, including combinations of different types of quotes but it didn't help. @finswimmer, thanks for the link, I'll check it :) ...
written 7 weeks ago by little_more10
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Comment: C: using GNU parallel for bwa mem and samtools
... Thank you so much for your solution! it seems to be exactly what I need but I get an error saying: /usr/bin/sh: line 1: mem: command not found I think it might be caused by the fact that I use a variable for calling bwa: bwa=/work/gr-fe/lawless/tool/bwa-0.7.17/bwa and then $bwa me ...
written 7 weeks ago by little_more10

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