User: ole.tange
ole.tange • 4.0k
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Posts by ole.tange
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... 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.tange • 4.0k
0
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3
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277
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... 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.tange • 4.0k
1
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3
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277
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... 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.tange • 4.0k
0
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3
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190
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3
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... 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.tange • 4.0k
4
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3
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190
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3
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... #!/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.tange • 4.0k
0
votes
0
answers
155
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Comment:
C: Using Parallel GNU
... Show us the output of `parallel --dry-run ...` ...
written 10 weeks ago by
ole.tange • 4.0k
1
vote
9
answers
122k
views
9
answers
... **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.tange • 4.0k
3
votes
2
answers
238
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2
answers
... @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.tange • 4.0k
3
votes
2
answers
497
views
2
answers
... parallel --plus "command -t {1} {2} {3} > {1}_{2/..}.out " ::: 4 8 ::: File1 File3 :::+ File2 File4 ...
written 6 months ago by
ole.tange • 4.0k
0
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2
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2.8k
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2
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... No need for `wait`. GNU Parallel does that for you. ...
written 6 months ago by
ole.tange • 4.0k
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