User: ole.tange

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ole.tange3.1k
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Posts by ole.tange

<prev • 77 results • page 1 of 8 • next >
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Comment: C: GNU parallel error: Command line too long
... I have found no way to increase the execve limit. ...
written 6 days ago by ole.tange3.1k
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Comment: C: GNU parallel error: Command line too long
... 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 7 days ago by ole.tange3.1k
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Answer: A: GNU parallel error: Command line too long
... 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 8 days ago by ole.tange3.1k
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Comment: C: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
... 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 28 days ago by ole.tange3.1k
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Comment: C: Are there any GNU parallel or similar Shell/Bash code examples on how to run Sna
... Or shorter: `ls *_1.fastq.gz | parallel --plus "bwa mem idx.fa {} {%_1.fastq.gz}_2.fastq.gz > {%_1.fastq.gz}.sam"` ...
written 9 weeks ago by ole.tange3.1k
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Answer: A: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
... 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 10 weeks ago by ole.tange3.1k
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Comment: C: GNU parallel on multiple files to re-header bam files
... I have not, but I am pretty sure the conclusion will be the same: It depends, and you should therefore test with different parallelization and measure. ...
written 12 weeks ago by ole.tange3.1k
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Comment: C: GNU parallel on multiple files to re-header bam files
... See also: https://oletange.wordpress.com/2015/07/04/parallel-disk-io-is-it-faster/ ...
written 12 weeks ago by ole.tange3.1k
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Answer: A: GNU parallel on multiple files to re-header bam files
... doit() { file="$1" out="$2" (samtools view -H $file | awk '(/^@SQ/ && /chrM/) || (!/^@SQ/) {print $0} '; samtools view $file) | samtools view -hb - > $out } export -f doit parallel doit {} {.}_filtered_re-header.bam ::: *.bam Or if you want to use ...
written 4 months ago by ole.tange3.1k
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Answer: A: How to parallelize fastq-dump command when reading SRA IDs from a .txt file?
... It is unclear to me what SRAIdFromPythonInput.txt contains. Can you give a couple of lines as example? doit() { i="$1" echo "$i" ./fastq-dump --split-files $i -v } export -f doit parallel doit :::: SRAIdFromPythonInput.txt ...
written 11 months ago by ole.tange3.1k

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Appreciated 6 days ago, created a post with more than 5 votes. For A: Gnu Parallel Quoting With Awk
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