User: ole.tange

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ole.tange4.0k
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Posts by ole.tange

<prev • 104 results • page 1 of 11 • next >
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Answer: A: Using GNU parallel to speed up merging VCFs with bcftools
... First: Learn `tmux`. This way you can let PuTTY crash, and you can reconnect and continue where you left off. It is also excellent for starting a job at work, and then reconnecting when you get home to see how it is doing. I use: `tmux`, `CTRL-b CTRL-c`, `CTRL-b CTRL-n`, `CTRL-b CTRL-p`, `CTRL-b CT ...
written 23 days ago by ole.tange4.0k
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Comment: C: concatenate all the files with matching prefix in a directory of several files
... By omitting `-j` GNU Parallel defaults to running one job per cpu thread. So similar to `-j $(nproc)`. Also you should probably use `>>` and not `>`. ...
written 26 days ago by ole.tange4.0k
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Answer: A: concatenate all the files with matching prefix in a directory of several files
... You are looking for https://www.gnu.org/software/parallel/man.html#EXAMPLE:-Aggregating-content-of-files parallel 'eval cat {= s/L001_R1/*/ =} > {= s/_L001_R1//=}' ::: *L001_R1.fastq This will run: cat HCOMB0001_ATTACTC-TATAGCC_*.fastq > HCOMB0001_ATTACTC-TATAGCC.fastq Check that i ...
written 26 days ago by ole.tange4.0k
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Comment: C: Is it possible to run haplotypecaller in gnu parallel ?
... Are you writing exactly what I wrote? Because if you change `#!/bin/bash` to `#!/bin/sh` then it will not work. ...
written 5 weeks ago by ole.tange4.0k
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Answer: A: Is it possible to run haplotypecaller in gnu parallel ?
... #!/bin/bash do_one() { gatk --java-options "-Xmx40g" HaplotypeCaller -R /media/gatk/Homo_sapiens_assembly38.fasta -I "$1" -O "$1".vcf.gz --dbsnp /media/gatk/dbsnp_138.hg38.vcf.gz -L /media/gatk/target/ag_V6_list.interval_list } export -f do_one # test that do_one works ...
written 6 weeks ago by ole.tange4.0k
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Comment: C: Using Parallel GNU
... Show us the output of `parallel --dry-run ...` ...
written 10 weeks ago by ole.tange4.0k
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Answer: A: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
... **EXAMPLE: grouping of lines** GNU Parallel > 20190522 can split piped input into chunks based on the value of a given field. You have input as: sampleID,chr1, ... sampleID,chr1, ... : sampleID,chr1, ... sampleID,chr2, ... : sampleID,chr2, ... sampleID,chr3, ... ...
written 12 weeks ago by ole.tange4.0k
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Answer: A: Is there anyway to get a unix parallel command to write to standard output
... @Pierre's and @Wouter's solutions should work for you. The problem is that this: parallel bcftools stats chr{}.bcf | grep "number of records:" | cut -f 4 > chr{}.txt ::: {1..22} is interpreted as this: parallel bcftools stats chr{}.bcf | grep "number of records:" | cut -f ...
written 3 months ago by ole.tange4.0k
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Answer: A: GNU parallel command with several multiple arguments
... parallel --plus "command -t {1} {2} {3} > {1}_{2/..}.out " ::: 4 8 ::: File1 File3 :::+ File2 File4 ...
written 6 months ago by ole.tange4.0k
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Comment: C: Bulk download of entire BioProject SRA
... No need for `wait`. GNU Parallel does that for you. ...
written 6 months ago by ole.tange4.0k

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Popular Question 6 months ago, created a question with more than 1,000 views. For Got Multiple Cpus? Activate Them With Gnu Parallel
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