User: ole.tange

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ole.tange3.2k
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Posts by ole.tange

<prev • 80 results • page 1 of 8 • next >
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Answer: A: HOMER parallel annotation for big .bed file
... 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 6 weeks ago by ole.tange3.2k
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Comment: C: Trim_galore on multiple fast.qz files: syntax problem
... `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 6 weeks ago by ole.tange3.2k
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Answer: A: Trim_galore on multiple fast.qz files: syntax problem
... 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 7 weeks ago by ole.tange3.2k
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Comment: C: GNU parallel error: Command line too long
... I have found no way to increase the execve limit. ...
written 8 weeks ago by ole.tange3.2k
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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 8 weeks ago by ole.tange3.2k
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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 weeks ago by ole.tange3.2k
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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 11 weeks ago by ole.tange3.2k
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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 3 months ago by ole.tange3.2k
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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 4 months ago by ole.tange3.2k
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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 4 months ago by ole.tange3.2k

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