User: ole.tange
ole.tange • 3.2k
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Posts by ole.tange
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... Can you elaborate in why you do not have that? Is your reason covered on https://oletange.wordpress.com/2018/03/28/excuses-for-not-installing-gnu-parallel/ ...
written 6 weeks ago by
ole.tange • 3.2k
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... Can you test if this works, too:
parallel -a ../Big_bed.bed --pipe-part --block -1 --fifo \
annotatePeaks.pl {} hg19 > ./../anno_chunks/{.}_annotated.txt
or this (slower):
parallel -a ../Big_bed.bed --pipe-part --block -1 --cat \
annotatePeaks.pl {} hg19 > ./../anno_chun ...
written 3 months ago by
ole.tange • 3.2k
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... `find` is used because OP used `find`.
Your solution will often give the same result, but will fail if the files are in subdirs inside path_to_fastq or if there are so many that they do not fit on a single command line.
...
written 3 months ago by
ole.tange • 3.2k
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... This:
find path_to_fastq -name "*_R1_001.fastq.gz" |
parallel -j 1 trim_galore --paired --fastqc -o trim_galore/ {} {= s/_R1_/_R2_/ =}
or:
find path_to_fastq -name "*_R1_001.fastq.gz" |
parallel --plus -j 1 trim_galore --paired --fastqc -o trim_galore/ {} {/_R1_/_R2_}
...
written 3 months ago by
ole.tange • 3.2k
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... I have found no way to increase the execve limit. ...
written 4 months ago by
ole.tange • 3.2k
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3
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621
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... The problem is in execve, which has the 128KB limit. In other words: It is not the same limit as you see in `getconf ARG_MAX`.
...
written 4 months ago by
ole.tange • 3.2k
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... GNU Parallel pessimistically assumes all characters have to be quoted. For this reason the max line length is half of what you would otherwise expect.
> I have a file with the commands to run (several thousand) and I pipe it to parallel. It seems one of these commands is way too big...
A comman ...
written 4 months ago by
ole.tange • 3.2k
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... Use Bash's builtin `printf`. Because it is builtin it is not subject to the same limit:
printf "%s\0" seq.* | parallel do something ...
written 4 months ago by
ole.tange • 3.2k
0
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... Or shorter: `ls *_1.fastq.gz | parallel --plus "bwa mem idx.fa {} {%_1.fastq.gz}_2.fastq.gz > {%_1.fastq.gz}.sam"`
...
written 6 months ago by
ole.tange • 3.2k
2
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10
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103k
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... The GNU Parallel 2018 book will be launched on 2018-05-11: https://www.prosa.dk/nc/arrangementer/arrangement/gnu-parallel-foredrag-og-boglancering/
But it can already be gotten at http://www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html
The source for the book is here: ...
written 6 months ago by
ole.tange • 3.2k
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