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From: | Andreas Bernauer |
Subject: | Re: GNU Parallel Bug Reports java flag being interpreted by bash, and 2+ extension chomping |
Date: | Fri, 21 Aug 2015 22:40:01 +0200 |
User-agent: | Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:38.0) Gecko/20100101 Thunderbird/38.2.0 |
On 21/08/15 19:55, Cameron Prybol wrote: > ``` > $ ./s13.variant_calibration.sh <http://s13.variant_calibration.sh> > /bin/bash: 2.0: No such file or directory > /bin/bash: 2.0: No such file or directory > [...] > ``` > > is breaking because of the --filterExpression "QD < 2.0" being > interpreted as a < file input in this command > > ``` > parallel java -jar $GATK -T VariantFiltration -R > "$REF_DIR/human_g1k_v37.fasta" -V {} -window 35 -cluster 3 --filterName > QD --filterExpression "QD < 2.0" --filterName FS --filterExpression "FS >> 30.0" -o "$VCF_OUT/"'{= s:.*/::; s:\.[^.]+$::; s:\.[^.]+$::; > =}'.filtered.vcf ::: "$(ls "$VCF_IN"/*.vcf)" > ``` You have to quote your redirection twice in this case: $ seq 2 | parallel echo "'QD < 2.0'" {} QD < 2.0 1 QD < 2.0 2 The first set of quotes is consumed by your shell that calls parallel. The second set of quotes prevents the called shell (or parallel? I'm not sure) to interpret the '<' as a redirect. -Andreas
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